diff --git a/_pkgdown.yml b/_pkgdown.yml
index d5463906634dae3c8efcb557e6a753393e53ce23..7da353f10dddc7efc64060ee37b857127c048215 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -52,8 +52,8 @@ reference:
   - title: Comparison functions
     desc: Functions for comparing datasets
     contents:
-      - '`compareSCESets`'
-      - '`diffSCESets`'
+      - '`compareSCEs`'
+      - '`diffSCEs`'
       - '`makeCompPanel`'
       - '`makeDiffPanel`'
       - '`makeOverallPanel`'
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 9961e50cc94558a0258ad34055ed2fbc3a95cbf6..a2ba076e3dde0657e8e82841529e0f05ec4d2d45 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -76,7 +76,7 @@
       <h1>Introduction to Splatter</h1>
                         <h4 class="author">Luke Zappia</h4>
             
-            <h4 class="date">2017-08-04</h4>
+            <h4 class="date">2017-09-13</h4>
           </div>
 
     
@@ -131,8 +131,38 @@
 ##     'browseVignettes()'. To cite Bioconductor, see
 ##     'citation("Biobase")', and for packages 'citation("pkgname")'.</code></pre>
 <pre><code>## Loading required package: ggplot2</code></pre>
+<pre><code>## Loading required package: SingleCellExperiment</code></pre>
+<pre><code>## Loading required package: SummarizedExperiment</code></pre>
+<pre><code>## Loading required package: GenomicRanges</code></pre>
+<pre><code>## Loading required package: stats4</code></pre>
+<pre><code>## Loading required package: S4Vectors</code></pre>
+<pre><code>## 
+## Attaching package: 'S4Vectors'</code></pre>
+<pre><code>## The following object is masked from 'package:base':
+## 
+##     expand.grid</code></pre>
+<pre><code>## Loading required package: IRanges</code></pre>
+<pre><code>## Loading required package: GenomeInfoDb</code></pre>
+<pre><code>## Loading required package: DelayedArray</code></pre>
+<pre><code>## Loading required package: matrixStats</code></pre>
+<pre><code>## 
+## Attaching package: 'matrixStats'</code></pre>
+<pre><code>## The following objects are masked from 'package:Biobase':
+## 
+##     anyMissing, rowMedians</code></pre>
+<pre><code>## 
+## Attaching package: 'DelayedArray'</code></pre>
+<pre><code>## The following objects are masked from 'package:matrixStats':
+## 
+##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</code></pre>
+<pre><code>## The following object is masked from 'package:base':
+## 
+##     apply</code></pre>
 <pre><code>## 
 ## Attaching package: 'scater'</code></pre>
+<pre><code>## The following object is masked from 'package:S4Vectors':
+## 
+##     rename</code></pre>
 <pre><code>## The following object is masked from 'package:stats':
 ## 
 ##     filter</code></pre>
@@ -149,7 +179,6 @@ sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSi
 <pre><code>## Simulating BCV...</code></pre>
 <pre><code>## Simulating counts..</code></pre>
 <pre><code>## Simulating dropout (if needed)...</code></pre>
-<pre><code>## Creating final SCESet...</code></pre>
 <pre><code>## Done!</code></pre>
 <p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
 </div>
@@ -288,7 +317,7 @@ params</code></pre></div>
 ## 
 ## Global: 
 ## (Genes)  (Cells)   [Seed]  
-##   10000      100    98513  
+##   10000      100   918851  
 ## 
 ## 27 additional parameters 
 ## 
@@ -361,7 +390,7 @@ params</code></pre></div>
 ## 
 ## Global: 
 ## (GENES)  (Cells)   [Seed]  
-##    8000      100    98513  
+##    8000      100   918851  
 ## 
 ## 27 additional parameters 
 ## 
@@ -434,7 +463,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 ## Gene_0004        0        1        0        0        0
 ## Gene_0005        0        0       11        0        0</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</code></pre></div>
-<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take an <code>SCESet</code> object from the <code>scater</code> package. The estimation process has the following steps:</p>
+<p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. The estimation process has the following steps:</p>
 <ol style="list-style-type: decimal">
 <li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
 <li>Library size parameters are estimated by fitting a log-normal distribution to the library sizes.</li>
@@ -456,67 +485,66 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <pre><code>## Simulating BCV...</code></pre>
 <pre><code>## Simulating counts..</code></pre>
 <pre><code>## Simulating dropout (if needed)...</code></pre>
-<pre><code>## Creating final SCESet...</code></pre>
 <pre><code>## Done!</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim</code></pre></div>
-<pre><code>## SCESet (storageMode: lockedEnvironment)
-## assayData: 1000 features, 40 samples 
-##   element names: BaseCellMeans, BatchCellMeans, BCV, CellMeans, counts, exprs, TrueCounts 
-## protocolData: none
-## phenoData
-##   sampleNames: Cell1 Cell2 ... Cell40 (40 total)
-##   varLabels: Cell Batch ExpLibSize
-##   varMetadata: labelDescription
-## featureData
-##   featureNames: Gene1 Gene2 ... Gene1000 (1000 total)
-##   fvarLabels: Gene BaseGeneMean OutlierFactor GeneMean
-##   fvarMetadata: labelDescription
-## experimentData: use 'experimentData(object)'
-## Annotation:</code></pre>
-<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is an <code>SCESet</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly an <code>SCESet</code> contains phenotype information about each cell (accessed using <code>pData</code>) and feature information about each gene (accessed using <code>fData</code>). Splatter uses these slots to store information about the intermediate values of the simulation.</p>
+<pre><code>## class: SingleCellExperiment 
+## dim: 1000 40 
+## metadata(1): params
+## assays(6): BatchCellMeans BaseCellMeans ... TrueCounts counts
+## rownames(1000): Gene1 Gene2 ... Gene999 Gene1000
+## rowData names(4): Gene BaseGeneMean OutlierFactor GeneMean
+## colnames(40): Cell1 Cell2 ... Cell39 Cell40
+## colData names(3): Cell Batch ExpLibSize
+## reducedDimNames(0):
+## spikeNames(0):</code></pre>
+<p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Access the counts</span>
 <span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
 <pre><code>##       Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1    71    18     0     0     0
-## Gene2     0   202    97     0    13
-## Gene3    76     0    70     0  4352
-## Gene4    13     0     0     0     0
-## Gene5   563    89    77     0    17</code></pre>
+## Gene1    94     0     0     0   102
+## Gene2     0    80     0    28     7
+## Gene3     0     1   321     4     0
+## Gene4     0     1   375     0     0
+## Gene5     0     0    42     1     0</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about genes</span>
-<span class="kw">head</span>(<span class="kw">fData</span>(sim))</code></pre></div>
-<pre><code>##        Gene BaseGeneMean OutlierFactor  GeneMean
-## Gene1 Gene1     12.15713             1  12.15713
-## Gene2 Gene2     24.31063             1  24.31063
-## Gene3 Gene3    297.25887             1 297.25887
-## Gene4 Gene4     59.50166             1  59.50166
-## Gene5 Gene5     22.53820             1  22.53820
-## Gene6 Gene6     20.61026             1  20.61026</code></pre>
+<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
+<pre><code>## DataFrame with 6 rows and 4 columns
+##       Gene BaseGeneMean OutlierFactor   GeneMean
+##   &lt;factor&gt;    &lt;numeric&gt;     &lt;numeric&gt;  &lt;numeric&gt;
+## 1    Gene1    20.190793             1  20.190793
+## 2    Gene2   315.498092             1 315.498092
+## 3    Gene3    40.235698             1  40.235698
+## 4    Gene4     3.595814             1   3.595814
+## 5    Gene5     1.504027             1   1.504027
+## 6    Gene6    41.998472             1  41.998472</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about cells</span>
-<span class="kw">head</span>(<span class="kw">pData</span>(sim))</code></pre></div>
-<pre><code>##        Cell  Batch ExpLibSize
-## Cell1 Cell1 Batch1   95909.41
-## Cell2 Cell2 Batch1  244118.47
-## Cell3 Cell3 Batch1  240747.25
-## Cell4 Cell4 Batch1  271459.87
-## Cell5 Cell5 Batch1  424160.08
-## Cell6 Cell6 Batch1  228110.31</code></pre>
+<span class="kw">head</span>(<span class="kw">colData</span>(sim))</code></pre></div>
+<pre><code>## DataFrame with 6 rows and 3 columns
+##           Cell       Batch ExpLibSize
+##       &lt;factor&gt; &lt;character&gt;  &lt;numeric&gt;
+## Cell1    Cell1      Batch1   285352.9
+## Cell2    Cell2      Batch1   237166.0
+## Cell3    Cell3      Batch1   133623.1
+## Cell4    Cell4      Batch1   278033.4
+## Cell5    Cell5      Batch1   272639.2
+## Cell6    Cell6      Batch1   302447.6</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Gene by cell matrices</span>
-<span class="kw">names</span>(<span class="kw">assayData</span>(sim))</code></pre></div>
-<pre><code>## [1] "TrueCounts"     "BaseCellMeans"  "BatchCellMeans" "counts"        
-## [5] "BCV"            "CellMeans"      "exprs"</code></pre>
+<span class="kw">names</span>(<span class="kw">assays</span>(sim))</code></pre></div>
+<pre><code>## [1] "BatchCellMeans" "BaseCellMeans"  "BCV"            "CellMeans"     
+## [5] "TrueCounts"     "counts"</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Example of cell means matrix</span>
-<span class="kw">get_exprs</span>(sim, <span class="st">"CellMeans"</span>)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
-<pre><code>##             Cell1        Cell2        Cell3        Cell4        Cell5
-## Gene1  65.5696590 1.391352e+01   0.06193530 2.453784e-02 1.355897e-03
-## Gene2   0.4790134 2.126821e+02 102.46301607 3.225135e-09 9.960240e+00
-## Gene3  67.4445673 4.695054e-05  71.05222310 6.950506e-11 4.334285e+03
-## Gene4  10.4052334 9.127828e-08   0.01250279 1.721067e-07 1.163755e-16
-## Gene5 556.8580925 8.854150e+01  67.68883291 1.097594e-06 1.449732e+01</code></pre>
-<p>An additional (big) advantage of outputting an <code>SCESet</code> is that we get immediate access to all of the <code>scater</code> functions. For example we can make a PCA plot:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim)</code></pre></div>
+<span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<pre><code>##              Cell1        Cell2        Cell3        Cell4        Cell5
+## Gene1 1.002071e+02 6.778755e-01 7.599324e-08 1.081554e-02 8.680064e+01
+## Gene2 2.358624e-03 8.386664e+01 6.321106e-02 2.583823e+01 8.731474e+00
+## Gene3 1.987226e-03 2.589992e-02 3.039511e+02 3.982977e+00 1.096817e-13
+## Gene4 1.173995e-08 2.266400e-01 3.745064e+02 2.686863e-32 1.253940e-01
+## Gene5 2.008658e-06 8.487400e-30 4.619085e+01 9.285997e-02 1.383831e-13</code></pre>
+<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
 <p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
-<p>For more details of the <code>SCESet</code> and what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
+<p>For more details about the <code>SingleCellExperiment</code> object refer to the <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
 <p>The <code>splatSimulate</code> function outputs the following additional information about the simulation:</p>
 <ul>
 <li>
@@ -565,7 +593,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 </ul>
 </li>
 </ul>
-<p>Values that have been added by Splatter are named using <code>UpperCamelCase</code> to separate them from the <code>underscore_naming</code> used by <code>scater</code>. For more information on the simulation see <code><a href="../reference/splatSimulate.html">?splatSimulate</a></code>.</p>
+<p>Values that have been added by Splatter are named using <code>UpperCamelCase</code> to separate them from the <code>underscore_naming</code> used by <code>scater</code> and other packages. For more information on the simulation see <code><a href="../reference/splatSimulate.html">?splatSimulate</a></code>.</p>
 <div id="simulating-groups" class="section level2">
 <h2 class="hasAnchor">
 <a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
@@ -573,7 +601,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,
                             <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</code></pre></div>
+<span class="kw">plotPCA</span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
 <p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
 </div>
@@ -582,7 +610,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
 <p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.paths &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</code></pre></div>
+<span class="kw">plotPCA</span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
 <p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>Here the colours represent the “step” of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
 </div>
@@ -591,12 +619,13 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <a href="#batch-effects" class="anchor"></a>Batch effects</h2>
 <p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.batches &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</code></pre></div>
+<span class="kw">plotPCA</span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
 <p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),
                             <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</code></pre></div>
+<span class="kw">plotPCA</span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>,
+        <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
 <p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
 </div>
@@ -713,40 +742,42 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 </tr>
 </tbody>
 </table>
-<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns an <code>SCESet</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">?lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
+<p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
 </div>
 <div id="other-expression-values" class="section level1">
 <h1 class="hasAnchor">
 <a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
-<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to an <code>SCESet</code> object but they require a length for each gene. The <code>addGeneLengths</code> can be used to simulate these lengths:</p>
+<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)
 sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)
-<span class="kw">head</span>(<span class="kw">fData</span>(sim))</code></pre></div>
-<pre><code>##        Gene     GeneMean Length
-## Gene1 Gene1 0.0002067453   1694
-## Gene2 Gene2 0.2420681809   1908
-## Gene3 Gene3 1.1117145796   6058
-## Gene4 Gene4 0.1920623085  15962
-## Gene5 Gene5 0.1872010591   3664
-## Gene6 Gene6 0.2867576121  12947</code></pre>
+<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
+<pre><code>## DataFrame with 6 rows and 3 columns
+##       Gene    GeneMean    Length
+##   &lt;factor&gt;   &lt;numeric&gt; &lt;numeric&gt;
+## 1    Gene1 0.486083183      1855
+## 2    Gene2 0.004635796      3158
+## 3    Gene3 0.401665079      1432
+## 4    Gene4 5.293414031      3396
+## 5    Gene5 0.022507485      2581
+## 6    Gene6 0.138698311      6003</code></pre>
 <p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) &lt;-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">fData</span>(sim)<span class="op">$</span>Length)
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) &lt;-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)
 <span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
-<pre><code>##          Cell1 Cell2    Cell3    Cell4 Cell5
-## Gene1  0.00000     0  0.00000  0.00000     0
-## Gene2  0.00000     0  0.00000  0.00000     0
-## Gene3 53.00124     0 26.08949 53.40399     0
-## Gene4  0.00000     0  0.00000  0.00000     0
-## Gene5 43.81571     0 43.13596  0.00000     0</code></pre>
+<pre><code>##          Cell1     Cell2    Cell3     Cell4    Cell5
+## Gene1   0.0000  82.60394  0.00000   0.00000   0.0000
+## Gene2   0.0000   0.00000  0.00000   0.00000   0.0000
+## Gene3 109.2362   0.00000  0.00000 105.56843   0.0000
+## Gene4 184.2476 315.84573 88.83347  44.51531 314.0713
+## Gene5   0.0000   0.00000  0.00000   0.00000   0.0000</code></pre>
 <p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
 </div>
 <div id="comparing-simulations-and-real-data" class="section level1">
 <h1 class="hasAnchor">
 <a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
-<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCESets</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SCESet</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
+<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim1 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
 sim2 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-comparison &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compareSCESets.html">compareSCESets</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))
+comparison &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))
 
 <span class="kw">names</span>(comparison)</code></pre></div>
 <pre><code>## [1] "FeatureData" "PhenoData"   "Plots"</code></pre>
@@ -765,8 +796,8 @@ comparison &lt;-<span class="st"> </span><span class="kw"><a href="../reference/
 <div id="comparing-differences" class="section level2">
 <h2 class="hasAnchor">
 <a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
-<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCESets</code> function. Similar to <code>compareSCESets</code> this function takes a list of <code>SCESet</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference &lt;-<span class="st"> </span><span class="kw"><a href="../reference/diffSCESets.html">diffSCESets</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)
+<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference &lt;-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)
 difference<span class="op">$</span>Plots<span class="op">$</span>Means</code></pre></div>
 <p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
@@ -816,7 +847,7 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">sessionInfo</span>()</code></pre></div>
 <pre><code>## R version 3.4.1 (2017-06-30)
 ## Platform: x86_64-apple-darwin15.6.0 (64-bit)
-## Running under: macOS Sierra 10.12.5
+## Running under: macOS Sierra 10.12.6
 ## 
 ## Matrix products: default
 ## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
@@ -826,56 +857,58 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
 ## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
 ## 
 ## attached base packages:
-## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
-## [8] base     
+## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
+## [8] methods   base     
 ## 
 ## other attached packages:
-## [1] splatter_1.1.4      scater_1.4.0        ggplot2_2.2.1      
-## [4] Biobase_2.36.2      BiocGenerics_0.22.0
+##  [1] splatter_1.1.4              scater_1.5.12              
+##  [3] SingleCellExperiment_0.99.3 SummarizedExperiment_1.7.6 
+##  [5] DelayedArray_0.3.19         matrixStats_0.52.2         
+##  [7] GenomicRanges_1.29.13       GenomeInfoDb_1.13.4        
+##  [9] IRanges_2.11.15             S4Vectors_0.15.7           
+## [11] ggplot2_2.2.1               Biobase_2.37.2             
+## [13] BiocGenerics_0.23.1        
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] viridis_0.4.0              edgeR_3.18.1              
-##  [3] splines_3.4.1              bit64_0.9-7               
-##  [5] viridisLite_0.2.0          shiny_1.0.3               
-##  [7] assertthat_0.2.0           highr_0.6                 
-##  [9] sp_1.2-5                   stats4_3.4.1              
-## [11] blob_1.1.0                 GenomeInfoDbData_0.99.0   
-## [13] vipor_0.4.5                yaml_2.1.14               
-## [15] RSQLite_2.0                backports_1.1.0           
-## [17] lattice_0.20-35            glue_1.1.1                
-## [19] limma_3.32.4               digest_0.6.12             
-## [21] XVector_0.16.0             GenomicRanges_1.28.4      
-## [23] checkmate_1.8.3            colorspace_1.3-2          
-## [25] cowplot_0.7.0              htmltools_0.3.6           
-## [27] httpuv_1.3.5               Matrix_1.2-10             
-## [29] plyr_1.8.4                 XML_3.98-1.9              
-## [31] pkgconfig_2.0.1            biomaRt_2.32.1            
-## [33] zlibbioc_1.22.0            xtable_1.8-2              
-## [35] scales_0.4.1               BiocParallel_1.10.1       
-## [37] tibble_1.3.3               IRanges_2.10.2            
-## [39] SummarizedExperiment_1.6.3 lazyeval_0.2.0            
-## [41] survival_2.41-3            magrittr_1.5              
-## [43] mime_0.5                   memoise_1.1.0             
-## [45] evaluate_0.10.1            MASS_7.3-47               
-## [47] beeswarm_0.2.3             shinydashboard_0.6.1      
-## [49] fitdistrplus_1.0-9         tools_3.4.1               
-## [51] data.table_1.10.4          matrixStats_0.52.2        
-## [53] stringr_1.2.0              S4Vectors_0.14.3          
-## [55] munsell_0.4.3              locfit_1.5-9.1            
-## [57] DelayedArray_0.2.7         AnnotationDbi_1.38.1      
-## [59] bindrcpp_0.2               akima_0.6-2               
-## [61] compiler_3.4.1             GenomeInfoDb_1.12.2       
-## [63] rlang_0.1.1.9000           rhdf5_2.20.0              
-## [65] grid_3.4.1                 RCurl_1.95-4.8            
-## [67] tximport_1.4.0             rjson_0.2.15              
-## [69] labeling_0.3               bitops_1.0-6              
-## [71] rmarkdown_1.6              gtable_0.2.0              
-## [73] DBI_0.7                    reshape2_1.4.2            
-## [75] R6_2.2.2                   gridExtra_2.2.1           
-## [77] knitr_1.16                 dplyr_0.7.2               
-## [79] bit_1.1-12                 bindr_0.1                 
-## [81] rprojroot_1.2              stringi_1.1.5             
-## [83] ggbeeswarm_0.5.3           Rcpp_0.12.12</code></pre>
+##  [1] viridis_0.4.0           edgeR_3.19.3           
+##  [3] splines_3.4.1           bit64_0.9-7            
+##  [5] viridisLite_0.2.0       shiny_1.0.5            
+##  [7] assertthat_0.2.0        highr_0.6              
+##  [9] sp_1.2-5                blob_1.1.0             
+## [11] GenomeInfoDbData_0.99.1 vipor_0.4.5            
+## [13] yaml_2.1.14             progress_1.1.2         
+## [15] RSQLite_2.0             backports_1.1.0        
+## [17] lattice_0.20-35         glue_1.1.1             
+## [19] limma_3.33.9            digest_0.6.12          
+## [21] checkmate_1.8.3         XVector_0.17.1         
+## [23] colorspace_1.3-2        cowplot_0.8.0          
+## [25] htmltools_0.3.6         httpuv_1.3.5           
+## [27] Matrix_1.2-11           plyr_1.8.4             
+## [29] XML_3.98-1.9            pkgconfig_2.0.1        
+## [31] biomaRt_2.33.4          zlibbioc_1.23.0        
+## [33] xtable_1.8-2            scales_0.5.0           
+## [35] BiocParallel_1.11.8     tibble_1.3.4           
+## [37] lazyeval_0.2.0          survival_2.41-3        
+## [39] magrittr_1.5            mime_0.5               
+## [41] memoise_1.1.0           evaluate_0.10.1        
+## [43] MASS_7.3-47             beeswarm_0.2.3         
+## [45] shinydashboard_0.6.1    fitdistrplus_1.0-9     
+## [47] tools_3.4.1             data.table_1.10.4      
+## [49] prettyunits_1.0.2       stringr_1.2.0          
+## [51] munsell_0.4.3           locfit_1.5-9.1         
+## [53] AnnotationDbi_1.39.3    bindrcpp_0.2           
+## [55] akima_0.6-2             compiler_3.4.1         
+## [57] rlang_0.1.2             rhdf5_2.21.4           
+## [59] grid_3.4.1              RCurl_1.95-4.8         
+## [61] tximport_1.5.0          rjson_0.2.15           
+## [63] labeling_0.3            bitops_1.0-6           
+## [65] rmarkdown_1.6           gtable_0.2.0           
+## [67] DBI_0.7                 reshape2_1.4.2         
+## [69] R6_2.2.2                gridExtra_2.3          
+## [71] knitr_1.17              dplyr_0.7.3            
+## [73] bit_1.1-12              bindr_0.1              
+## [75] rprojroot_1.2           stringi_1.1.5          
+## [77] ggbeeswarm_0.6.0        Rcpp_0.12.12</code></pre>
 </div>
 </div>
   </div>
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diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index ba93ed5f12158b6d3eeef5a1d86dc8e6dcff222e..09f2c7d45453b831d5795b704ef917265ec4d296 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -102,7 +102,7 @@
     </div>
 
     
-    <p>Add additional feature statistics to an SCESet object</p>
+    <p>Add additional feature statistics to a SingleCellExperiment object</p>
     
 
     <pre class="usage"><span class='fu'>addFeatureStats</span>(<span class='no'>sce</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"counts"</span>, <span class='st'>"cpm"</span>, <span class='st'>"tpm"</span>, <span class='st'>"fpkm"</span>), <span class='kw'>log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
@@ -113,13 +113,13 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sce</th>
-      <td><p>SCESet to add feature statistics to.</p></td>
+      <td><p>SingleCellExperiment to add feature statistics to.</p></td>
     </tr>
     <tr>
       <th>value</th>
       <td><p>the expression value to calculate statistics for. Options are
 "counts", "cpm", "tpm" or "fpkm". The values need to exist in the
-given SCESet.</p></td>
+given SingleCellExperiment.</p></td>
     </tr>
     <tr>
       <th>log</th>
@@ -138,16 +138,16 @@ calculating statistics.</p></td>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with additional feature statistics</p>
+    <p>SingleCellExperiment with additional feature statistics</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>Currently adds the following statistics: mean, variance, coefficient of
 variation, median and median absolute deviation. Statistics are added to
-the <code>fData</code> slot and are named <code>Stat[Log]Value[No0]</code> where
-<code>Log</code> and <code>No0</code> are added if those arguments are true.
-UpperCamelCase is used to differentiate these columns from those added by
-<code>scater</code>.</p>
+the <code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/SummarizedExperiment-class'>rowData</a></code> slot and are named
+<code>Stat[Log]Value[No0]</code> where <code>Log</code> and <code>No0</code> are added if those
+arguments are true. UpperCamelCase is used to differentiate these columns
+from those added by analysis packages.</p>
     
 
   </div>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index 72ab65f1a34c2f215e73a45b6d6409931691c45e..cf91405e96a43f9352d209d4957d0aaf97c56d7b 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -102,7 +102,7 @@
     </div>
 
     
-    <p>Add gene lengths to an SCESet object</p>
+    <p>Add gene lengths to an SingleCellExperiment object</p>
     
 
     <pre class="usage"><span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"generate"</span>, <span class='st'>"sample"</span>), <span class='kw'>loc</span> <span class='kw'>=</span> <span class='fl'>7.9</span>,
@@ -113,7 +113,7 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sce</th>
-      <td><p>SCESet to add gene lengths to.</p></td>
+      <td><p>SingleCellExperiment to add gene lengths to.</p></td>
     </tr>
     <tr>
       <th>method</th>
@@ -135,29 +135,33 @@
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with added gene lengths</p>
+    <p>SingleCellExperiment with added gene lengths</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>This function adds simulated gene lengths to the <code>fData</code> slot of an
-<code>SCESet</code> object that can be used for calculating length normalised
-expression values such as TPM or FPKM. The <code>generate</code> simulates lengths
-using a (rounded) log-normal distribution, with the default <code>loc</code> and
-<code>scale</code> parameters based on human coding genes. Alternatively the
-<code>sample</code> method can be used which randomly samples lengths (with
-replacement) from a supplied vector.</p>
+    <p>This function adds simulated gene lengths to the
+<code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/SummarizedExperiment-class'>rowData</a></code> slot of a
+<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that can be
+used for calculating length normalised expression values such as TPM or FPKM.
+The <code>generate</code> method simulates lengths using a (rounded) log-normal
+distribution, with the default <code>loc</code> and <code>scale</code> parameters based
+on human protein-coding genes. Alternatively the <code>sample</code> method can be
+used which randomly samples lengths (with replacement) from a supplied
+vector.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># Default generate method</span>
-<span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
-<span class='fu'>head</span>(<span class='fu'>fData</span>(<span class='no'>sce</span>))</div><div class='output co'>#&gt;        Gene   GeneMean Length
-#&gt; Gene1 Gene1 2.48516793   4364
-#&gt; Gene2 Gene2 2.66764544   2293
-#&gt; Gene3 Gene3 1.63746271   1981
-#&gt; Gene4 Gene4 5.95066226   8532
-#&gt; Gene5 Gene5 1.79688466   2083
-#&gt; Gene6 Gene6 0.09561467   3011</div><div class='input'># Sample method (human coding genes)
+<span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
+<span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#&gt; DataFrame with 6 rows and 3 columns
+#&gt;       Gene    GeneMean    Length
+#&gt;   &lt;factor&gt;   &lt;numeric&gt; &lt;numeric&gt;
+#&gt; 1    Gene1 0.001748482      1527
+#&gt; 2    Gene2 0.040891176      4195
+#&gt; 3    Gene3 0.027987949     15546
+#&gt; 4    Gene4 1.004302577      5228
+#&gt; 5    Gene5 2.437182383      1591
+#&gt; 6    Gene6 0.794571297      2089</div><div class='input'># Sample method (human coding genes)
 </div><span class='co'># NOT RUN {</span>
 <span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
 <span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
new file mode 100644
index 0000000000000000000000000000000000000000..d1ec1daae19d927f28f5e2ef4c7ba2a1237eefd7
--- /dev/null
+++ b/docs/reference/compareSCEs.html
@@ -0,0 +1,205 @@
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+    <div class="page-header">
+    <h1>Compare SingleCellExperiment objects</h1>
+    </div>
+
+    
+    <p>Combine the data from several SingleCellExperiment objects and produce some
+basic plots comparing them.</p>
+    
+
+    <pre class="usage"><span class='fu'>compareSCEs</span>(<span class='no'>sces</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>sces</th>
+      <td><p>named list of SingleCellExperiment objects to combine and
+compare.</p></td>
+    </tr>
+    <tr>
+      <th>point.size</th>
+      <td><p>size of points in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>point.alpha</th>
+      <td><p>opacity of points in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>fits</th>
+      <td><p>whether to include fits in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>colours</th>
+      <td><p>vector of colours to use for each dataset.</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>List containing the combined datasets and plots.</p>
+    
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>The returned list has three items:</p><dl class='dl-horizontal'>
+    <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+    SingleCellExperiments.</p></dd>
+    <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+    SingleCellExperiments.</p></dd>
+    <dt><code>Plots</code></dt><dd><p>Comparison plots
+        <dl class='dl-horizontal'>
+            <dt><code>Means</code></dt><dd><p>Boxplot of mean distribution.</p></dd>
+            <dt><code>Variances</code></dt><dd><p>Boxplot of variance distribution.</p></dd>
+            <dt><code>MeanVar</code></dt><dd><p>Scatter plot with fitted lines showing the
+            mean-variance relationship.</p></dd>
+            <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+            distribution.</p></dd>
+            <dt><code>ZerosGene</code></dt><dd><p>Boxplot of the percentage of each gene
+            that is zero.</p></dd>
+            <dt><code>ZerosCell</code></dt><dd><p>Boxplot of the percentage of each cell
+            that is zero.</p></dd>
+            <dt><code>MeanZeros</code></dt><dd><p>Scatter plot with fitted lines showing
+            the mean-zeros relationship.</p></dd>
+    </dl></p></dd>
+</dl>
+    <p>The plots returned by this function are created using
+<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+might like to consider. The data used to create these plots is also returned
+and should be in the correct format to allow you to create further plots
+using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#&gt; [1] "FeatureData" "PhenoData"   "Plots"      </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
+#&gt; [6] "ZerosCell"    "MeanZeros"   </div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#details">Details</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
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diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
new file mode 100644
index 0000000000000000000000000000000000000000..500f55f6e2ccb6fc2ffb7477b6b443d6092ed1bf
--- /dev/null
+++ b/docs/reference/diffSCEs.html
@@ -0,0 +1,227 @@
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+    <div class="page-header">
+    <h1>Diff SingleCellExperiment objects</h1>
+    </div>
+
+    
+    <p>Combine the data from several SingleCellExperiment objects and produce some
+basic plots comparing them to a reference.</p>
+    
+
+    <pre class="usage"><span class='fu'>diffSCEs</span>(<span class='no'>sces</span>, <span class='no'>ref</span>, <span class='kw'>point.size</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>fits</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>colours</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>sces</th>
+      <td><p>named list of SingleCellExperiment objects to combine and
+compare.</p></td>
+    </tr>
+    <tr>
+      <th>ref</th>
+      <td><p>string giving the name of the SingleCellExperiment to use as the
+reference</p></td>
+    </tr>
+    <tr>
+      <th>point.size</th>
+      <td><p>size of points in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>point.alpha</th>
+      <td><p>opacity of points in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>fits</th>
+      <td><p>whether to include fits in scatter plots.</p></td>
+    </tr>
+    <tr>
+      <th>colours</th>
+      <td><p>vector of colours to use for each dataset.</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>List containing the combined datasets and plots.</p>
+    
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>This function aims to look at the differences between a reference
+SingleCellExperiment and one or more others. It requires each
+SingleCellExperiment to have the same dimensions. Properties are compared by
+ranks, for example when comparing the means the values are ordered and the
+differences between the reference and another dataset plotted. A series of
+Q-Q plots are also returned.</p>
+<p>The returned list has five items:</p><dl class='dl-horizontal'>
+    <dt><code>Reference</code></dt><dd><p>The SingleCellExperiment used as the reference.</p></dd>
+    <dt><code>FeatureData</code></dt><dd><p>Combined feature data from the provided
+    SingleCellExperiments.</p></dd>
+    <dt><code>PhenoData</code></dt><dd><p>Combined pheno data from the provided
+    SingleCellExperiments.</p></dd>
+    <dt><code>Plots</code></dt><dd><p>Difference plots
+        <dl class='dl-horizontal'>
+            <dt><code>Means</code></dt><dd><p>Boxplot of mean differences.</p></dd>
+            <dt><code>Variances</code></dt><dd><p>Boxplot of variance differences.</p></dd>
+            <dt><code>MeanVar</code></dt><dd><p>Scatter plot showing the difference from
+            the reference variance across expression ranks.</p></dd>
+            <dt><code>LibraySizes</code></dt><dd><p>Boxplot of the library size
+            differences.</p></dd>
+            <dt><code>ZerosGene</code></dt><dd><p>Boxplot of the differences in the
+            percentage of each gene that is zero.</p></dd>
+            <dt><code>ZerosCell</code></dt><dd><p>Boxplot of the differences in the
+            percentage of each cell that is zero.</p></dd>
+            <dt><code>MeanZeros</code></dt><dd><p>Scatter plot showing the difference from
+            the reference percentage of zeros across expression ranks.</p></dd>
+    </dl></p></dd>
+  <dt><code>QQPlots</code></dt><dd><p>Quantile-Quantile plots
+      <dl class='dl-horizontal'>
+          <dt><code>Means</code></dt><dd><p>Q-Q plot of the means.</p></dd>
+          <dt><code>Variances</code></dt><dd><p>Q-Q plot of the variances.</p></dd>
+          <dt><code>LibrarySizes</code></dt><dd><p>Q-Q plot of the library sizes.</p></dd>
+          <dt><code>ZerosGene</code></dt><dd><p>Q-Q plot of the percentage of zeros per
+          gene.</p></dd>
+          <dt><code>ZerosCell</code></dt><dd><p>Q-Q plot of the percentage of zeros per
+          cell.</p></dd>
+      </dl></p></dd>
+</dl>
+    <p>The plots returned by this function are created using
+<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+might like to consider. The data used to create these plots is also returned
+and should be in the correct format to allow you to create further plots
+using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#&gt; [1] "Reference"   "FeatureData" "PhenoData"   "Plots"       "QQPlots"    </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
+#&gt; [6] "ZerosCell"    "MeanZeros"   </div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#details">Details</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 297b2526cd16dd579d8b2f4fc3e2feb429358fd1..2641e2e91223379618032bd4effb2b8d2058efd0 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -356,15 +356,15 @@
         <tr>
           <!--  -->
           <td>
-            <p><code><a href="compareSCESets.html">compareSCESets</a></code> </p>
+            <p><code><a href="compareSCEs.html">compareSCEs</a></code> </p>
           </td>
-          <td><p>Compare SCESet objects</p></td>
+          <td><p>Compare SingleCellExperiment objects</p></td>
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="diffSCESets.html">diffSCESets</a></code> </p>
+            <p><code><a href="diffSCEs.html">diffSCEs</a></code> </p>
           </td>
-          <td><p>Diff SCESet objects</p></td>
+          <td><p>Diff SingleCellExperiment objects</p></td>
         </tr><tr>
           <!--  -->
           <td>
@@ -388,7 +388,7 @@
           <td>
             <p><code><a href="summariseDiff.html">summariseDiff</a></code> </p>
           </td>
-          <td><p>Summarise diffSCESets</p></td>
+          <td><p>Summarise diffSCESs</p></td>
         </tr>
       </tbody><tbody>
         <tr>
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 4ce558477500f810f049d8006ff764609b774016..981a52b6ac4c56dfcd1225dba9d2fb704891fdb6 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -108,9 +108,10 @@
     <pre class="usage"><span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
 
-<span class='co'># S3 method for SCESet</span>
-<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
-  <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>,
+  <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(), <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>200</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
 
 <span class='co'># S3 method for matrix</span>
 <span class='fu'>lun2Estimate</span>(<span class='no'>counts</span>, <span class='no'>plates</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLun2Params</a></span>(),
@@ -121,8 +122,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>plates</th>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index e7c8f353a2e85124b011ad2538deb5f8f5b32e63..45a0e132d172bd313e7df72664db785261ed9e05 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -133,7 +133,7 @@ analyses of single-cell RNA-seq data".</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet containing simulated counts.</p>
+    <p>SingleCellExperiment containing simulated counts.</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -160,7 +160,7 @@ expression analyses of single-cell RNA-seq data. bioRxiv (2016).</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Simulating plate means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating libray size factors...</span></div><div class='output co'>#&gt; <span class='message'>Simulating cell means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div></pre>
+    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>lun2Simulate</span>()</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Simulating plate means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating libray size factors...</span></div><div class='output co'>#&gt; <span class='message'>Simulating cell means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index e6179fcf2decc9c11166660fbe7cc26373f6b377..3fe61bba91010a00ad7778c72a461637664bc418 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -107,7 +107,7 @@
 
     <pre class="usage"><span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
 
-<span class='co'># S3 method for SCESet</span>
+<span class='co'># S3 method for SingleCellExperiment</span>
 <span class='fu'>lunEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newLunParams</a></span>())
 
 <span class='co'># S3 method for matrix</span>
@@ -118,8 +118,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or an SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -146,7 +146,7 @@ for more details on the parameters.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40    88458  
+#&gt;    2000       40   213034  
 #&gt; 
 #&gt; 9 additional parameters 
 #&gt; 
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index 7b1880707433b09b06089757dfd99a9d3a077099..31bd82a4d9e1a77d385931ac948c4b4f0b203d45 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -129,8 +129,8 @@ sequencing data with many zero counts".</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet object containing the simulated counts and intermediate
-values.</p>
+    <p>SingleCellExperiment object containing the simulated counts and
+intermediate values.</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -151,7 +151,7 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>lunSimulate</span>()</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating cell means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='input'>
+    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>lunSimulate</span>()</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating cell means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index fae7764cfe2bbb90a11e412acc4d4865d5ccbf6a..952d7e03ae0fa742e966137455968c5a238f335d 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -102,7 +102,7 @@
     </div>
 
     
-    <p>Combine the plots from <code>compareSCESets</code> into a single panel.</p>
+    <p>Combine the plots from <code>compareSCEs</code> into a single panel.</p>
     
 
     <pre class="usage"><span class='fu'>makeCompPanel</span>(<span class='no'>comp</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>, <span class='st'>"Variance"</span>,
@@ -114,7 +114,7 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>comp</th>
-      <td><p>list returned by <code><a href='compareSCESets.html'>compareSCESets</a></code>.</p></td>
+      <td><p>list returned by <code><a href='compareSCEs.html'>compareSCEs</a></code>.</p></td>
     </tr>
     <tr>
       <th>title</th>
@@ -135,7 +135,7 @@
     <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
 <span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='compareSCESets.html'>compareSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
+<span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='compareSCEs.html'>compareSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
 <span class='no'>panel</span> <span class='kw'>&lt;-</span> <span class='fu'>makeCompPanel</span>(<span class='no'>comparison</span>)
 <span class='co'># }</span><div class='input'>
 </div></pre>
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index 2c9b51810684f4abd2cb1d95e3f0505db7f779a4..91a4c2ecf2af1fea4bfafd7d2375870fc006cfbe 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -102,7 +102,7 @@
     </div>
 
     
-    <p>Combine the plots from <code>diffSCESets</code> into a single panel.</p>
+    <p>Combine the plots from <code>diffSCEs</code> into a single panel.</p>
     
 
     <pre class="usage"><span class='fu'>makeDiffPanel</span>(<span class='no'>diff</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Difference comparison"</span>, <span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Means"</span>,
@@ -114,7 +114,7 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>diff</th>
-      <td><p>list returned by <code><a href='diffSCESets.html'>diffSCESets</a></code>.</p></td>
+      <td><p>list returned by <code><a href='diffSCEs.html'>diffSCEs</a></code>.</p></td>
     </tr>
     <tr>
       <th>title</th>
@@ -135,7 +135,7 @@
     <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
 <span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
-<span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
 <span class='no'>panel</span> <span class='kw'>&lt;-</span> <span class='fu'>makeDiffPanel</span>(<span class='no'>difference</span>)
 <span class='co'># }</span><div class='input'>
 </div></pre>
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 105774d5d22e814c88ecbabfbc7b3ee7a79a52cf..78c41a557bd16aaf909c25a023c2fe4f491356b8 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -102,7 +102,7 @@
     </div>
 
     
-    <p>Combine the plots from <code>compSCESets</code> and <code>diffSCESets</code> into a
+    <p>Combine the plots from <code>compSCEs</code> and <code>diffSCEs</code> into a
 single panel.</p>
     
 
@@ -116,11 +116,11 @@ single panel.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>comp</th>
-      <td><p>list returned by <code><a href='compareSCESets.html'>compareSCESets</a></code>.</p></td>
+      <td><p>list returned by <code><a href='compareSCEs.html'>compareSCEs</a></code>.</p></td>
     </tr>
     <tr>
       <th>diff</th>
-      <td><p>list returned by <code><a href='diffSCESets.html'>diffSCESets</a></code>.</p></td>
+      <td><p>list returned by <code><a href='diffSCEs.html'>diffSCEs</a></code>.</p></td>
     </tr>
     <tr>
       <th>title</th>
@@ -142,7 +142,7 @@ single panel.</p>
 <span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
 <span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)
 <span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compSCESets</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
-<span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+<span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'>diffSCESets</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
 <span class='no'>panel</span> <span class='kw'>&lt;-</span> <span class='fu'>makeOverallPanel</span>(<span class='no'>comparison</span>, <span class='no'>difference</span>)
 <span class='co'># }</span><div class='input'>
 </div></pre>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 6d47efec794d013b6f06c593c92a5a6557c15a6b..7aa9f16e76fce71d06249c6185a66b9e3e25ef52 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -108,9 +108,9 @@
     <pre class="usage"><span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
 
-<span class='co'># S3 method for SCESet</span>
-<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
-  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>,
+  <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>BPPARAM</span> <span class='kw'>=</span> <span class='fu'>SerialParam</span>())
 
 <span class='co'># S3 method for matrix</span>
 <span class='fu'>scDDEstimate</span>(<span class='no'>counts</span>, <span class='no'>conditions</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSCDDParams</a></span>(),
@@ -121,8 +121,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>conditions</th>
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index 7375ccad46ddc46e9abadf7b783673286a183447..397d4b5a9be488614c20e026080bb59adc9dee3c 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -143,14 +143,15 @@ giving the parallel back-end to be used. Default is
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet containing simulated counts</p>
+    <p>SingleCellExperiment containing simulated counts</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> that
 takes a <code><a href='SCDDParams.html'>SCDDParams</a></code>, runs the simulation then converts the
-output to an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object. See
-<code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more details of how the simulation works.</p>
+output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
+See <code><a href='http://www.rdocumentation.org/packages/scDD/topics/simulateSet'>simulateSet</a></code> for more details about how the simulation
+works.</p>
     
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 827501fd893943cfb93ef3b87751f3e733f85d25..88db9b4b7d6dc70c09bc4bf2a2c6c9cd754797b7 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -151,7 +151,7 @@
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (Cells)   [Seed]  
-#&gt;     100      100    88458  
+#&gt;     100      100   213034  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index a4d4f35230e5b688d40edb43b22a3f9db8372df8..9766768721e381d286108015de59f223c5f67406 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -146,7 +146,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (Genes)  (Cells)   [Seed]  
-#&gt;   10000      100    88458  
+#&gt;   10000      100   213034  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -164,7 +164,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    1000       50    88458  
+#&gt;    1000       50   213034  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -182,7 +182,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    1000       50    88458  
+#&gt;    1000       50   213034  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index b9a4cc3a3e173cbccc43f67bc342d104e565f270..fffcb0f33b34201bbe38371114c37b8712b3df64 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -107,8 +107,9 @@
 
     <pre class="usage"><span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
 
-<span class='co'># S3 method for SCESet</span>
-<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>,
+  <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())
 
 <span class='co'># S3 method for matrix</span>
 <span class='fu'>simpleEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSimpleParams</a></span>())</pre>
@@ -118,8 +119,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -148,7 +149,7 @@ details on the parameters.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40    88458  
+#&gt;    2000       40   213034  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index d86c2155aff536291fdd5c77dac8bb55e8222af1..e96bf35ffcf92fb3721137a2e7c1c313a0e24c6b 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -128,7 +128,7 @@ simulated library sizes, differential expression etc.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet containing simulated counts</p>
+    <p>SingleCellExperiment containing simulated counts</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -140,8 +140,8 @@ details of the parameters.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>simpleSimulate</span>()</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='co'># Override default parameters</span>
-<span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>simpleSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div></pre>
+    <pre class="examples"><div class='input'><span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>simpleSimulate</span>()</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='co'># Override default parameters</span>
+<span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>simpleSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 1d4eb2254d070d68a0b375f89dfa13fb39392f6f..dde62f166c26d0632f5e89d6a6fa68c4e2a78862 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -109,8 +109,9 @@ is done.</p>
 
     <pre class="usage"><span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
 
-<span class='co'># S3 method for SCESet</span>
-<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>splatEstimate</span>(<span class='no'>counts</span>,
+  <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())
 
 <span class='co'># S3 method for matrix</span>
 <span class='fu'>splatEstimate</span>(<span class='no'>counts</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newSplatParams</a></span>())</pre>
@@ -120,8 +121,8 @@ is done.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -148,7 +149,7 @@ data to estimate parameters from.</p></td>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40    88458  
+#&gt;    2000       40   213034  
 #&gt; 
 #&gt; 27 additional parameters 
 #&gt; 
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index ba6bfcfd7b8096389736750ec83125f02a4e820b..7e0c42284bda2151802ffbaf65c12907050e6088 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -114,7 +114,7 @@ and inverse gamma distribution.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add BCV means to.</p></td>
+      <td><p>SingleCellExperiment to add BCV means to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -124,7 +124,7 @@ and inverse gamma distribution.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated BCV means.</p>
+    <p>SingleCellExperiment with simulated BCV means.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index 1e8a32134a02cae13309c2e59021a388fca4e37d..5600e9430a9763870a8e484db31f1828f4e99360 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -113,7 +113,7 @@ factors.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add batch means to.</p></td>
+      <td><p>SingleCellExperiment to add batch means to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -123,7 +123,7 @@ factors.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated batch means.</p>
+    <p>SingleCellExperiment with simulated batch means.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 5eb6fb530e23bd8e93dbebe4591b2f5d4426058a..1b059e35b8c711fffb44d4d684d12683336b118b 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -114,7 +114,7 @@ means for each batch.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add batch effects to.</p></td>
+      <td><p>SingleCellExperiment to add batch effects to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -124,7 +124,7 @@ means for each batch.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated batch effects.</p>
+    <p>SingleCellExperiment with simulated batch effects.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index 605d3bf8e2231b1dce578fcb0f9afd8cead309c0..cb90535a07415a3082bcb67920746df4b51a36fb 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -120,7 +120,7 @@ means are adjusted for each cell's expected library size.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add cell means to.</p></td>
+      <td><p>SingleCellExperiment to add cell means to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -130,7 +130,7 @@ means are adjusted for each cell's expected library size.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with added cell means.</p>
+    <p>SingleCellExperiment with added cell means.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index cd926d7423465df0d414a504243ac3f9b4d53f1f..cf9c9e94befc0a78e6c3baf2a105a1abb182e9d1 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -117,7 +117,7 @@ they are simulated in the correct order.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add differential expression to.</p></td>
+      <td><p>SingleCellExperiment to add differential expression to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -127,7 +127,7 @@ they are simulated in the correct order.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated differential expression.</p>
+    <p>SingleCellExperiment with simulated differential expression.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index 612b648e40a1133872889011c0635498fac631a9..bcff9a23311d82a515e78c857e8308e2a4f1e8e1 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -115,7 +115,7 @@ to decide which counts should be dropped.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add dropout to.</p></td>
+      <td><p>SingleCellExperiment to add dropout to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -125,7 +125,7 @@ to decide which counts should be dropped.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated dropout and observed counts.</p>
+    <p>SingleCellExperiment with simulated dropout and observed counts.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index 47e35873077508b238454b03307f07be7b0b7672..4ac63ab88bb97720a9b86ae8b1c5725ede40217d 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -114,7 +114,7 @@ with the median mean expression multiplied by the outlier factor.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add gene means to.</p></td>
+      <td><p>SingleCellExperiment to add gene means to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -124,7 +124,7 @@ with the median mean expression multiplied by the outlier factor.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated gene means.</p>
+    <p>SingleCellExperiment with simulated gene means.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index e10e335cdd49d717b5bc4f9ccf8d01e73c699e32..a8cb353d521c96b48d71dfd4e0d8be4a5047de98 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -112,7 +112,7 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add library size to.</p></td>
+      <td><p>SingleCellExperiment to add library size to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -122,7 +122,7 @@
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated library sizes.</p>
+    <p>SingleCellExperiment with simulated library sizes.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 5d8336b638dadda262bdaf5653a72a494d0b22be..6f0ed0f8f1ede60ff8a6ec4189dbabc5ad652cd4 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -114,7 +114,7 @@ group (or path position), expected library size and BCV.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>sim</th>
-      <td><p>SCESet to add true counts to.</p></td>
+      <td><p>SingleCellExperiment to add true counts to.</p></td>
     </tr>
     <tr>
       <th>params</th>
@@ -124,7 +124,7 @@ group (or path position), expected library size and BCV.</p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet with simulated true counts.</p>
+    <p>SingleCellExperiment with simulated true counts.</p>
     
 
   </div>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index 653dd21293154347f70faadd19a531043a83336a..85d30845689ac5af5f256576e1f8b912cb9c5c72 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -143,8 +143,8 @@ trajectories (eg. differentiation processes).</p></td>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>SCESet object containing the simulated counts and intermediate
-values.</p>
+    <p>SingleCellExperiment object containing the simulated counts and
+intermediate values.</p>
     
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
@@ -163,14 +163,15 @@ can be used.</p>
 <li><p>Simulate BCV adjusted cell means</p></li>
 <li><p>Simulate true counts</p></li>
 <li><p>Simulate dropout</p></li>
-<li><p>Create final SCESet object</p></li>
+<li><p>Create final dataset</p></li>
 </ol>
-    <p>The final output is an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object that contains the
-simulated counts but also the values for various intermediate steps. These
-are stored in the <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/phenoData'>phenoData</a></code> (for cell specific
-information), <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/featureData'>featureData</a></code> (for gene specific
-information) or <code><a href='http://www.rdocumentation.org/packages/Biobase/topics/assayData'>assayData</a></code> (for gene by cell matrices)
-slots. This additional information includes:</p><dl class='dl-horizontal'>
+    <p>The final output is a
+<code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object that
+contains the simulated counts but also the values for various intermediate
+steps. These are stored in the <code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/SummarizedExperiment-class'>colData</a></code>
+(for cell specific information), <code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/SummarizedExperiment-class'>rowData</a></code>
+(for gene specific information) or <code><a href='http://www.rdocumentation.org/packages/SummarizedExperiment/topics/SummarizedExperiment-class'>assays</a></code>
+(for gene by cell matrices) slots. This additional information includes:</p><dl class='dl-horizontal'>
     <dt><code>phenoData</code></dt><dd><p><dl class='dl-horizontal'>
             <dt>Cell</dt><dd><p>Unique cell identifier.</p></dd>
             <dt>Group</dt><dd><p>The group or path the cell belongs to.</p></dd>
@@ -206,9 +207,9 @@ slots. This additional information includes:</p><dl class='dl-horizontal'>
             dropped in which cells.</p></dd>
         </dl></p></dd>
 </dl>
-    <p>Values that have been added by Splatter are named using <code>CamelCase</code> in
-order to differentiate them from the values added by Scater which uses
-<code>underscore_naming</code>.</p>
+    <p>Values that have been added by Splatter are named using <code>UpperCamelCase</code>
+in order to differentiate them from the values added by analysis packages
+which typically use <code>underscore_naming</code>.</p>
     
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
@@ -220,9 +221,8 @@ order to differentiate them from the values added by Scater which uses
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'># Simulation with default parameters
-</div><span class='co'># NOT RUN {</span>
-<span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>splatSimulate</span>()
+    <pre class="examples"><div class='input'><span class='co'># Simulation with default parameters</span>
+<span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>splatSimulate</span>()</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><span class='co'># NOT RUN {</span>
 <span class='co'># Simulation with different number of genes</span>
 <span class='no'>sim</span> <span class='kw'>&lt;-</span> <span class='fu'>splatSimulate</span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>)
 <span class='co'># Simulation with custom parameters</span>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index c1c76331d8941568792a8d176c4a151e76c5fea1..6a2d6fd25baee007759619e231e69a2165b4f44e 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Summarise diffSCESets — summariseDiff • Splatter</title>
+<title>Summarise diffSCESs — summariseDiff • Splatter</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -98,11 +98,11 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Summarise diffSCESets</h1>
+    <h1>Summarise diffSCESs</h1>
     </div>
 
     
-    <p>Summarise the results of <code><a href='diffSCESets.html'>diffSCESets</a></code>. Calculates the Median
+    <p>Summarise the results of <code><a href='diffSCEs.html'>diffSCEs</a></code>. Calculates the Median
 Absolute Deviation (MAD), Mean Absolute Error (MAE) and Root Mean Squared
 Error (RMSE) for the various properties and ranks them.</p>
     
@@ -114,7 +114,7 @@ Error (RMSE) for the various properties and ranks them.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>diff</th>
-      <td><p>Output from <code><a href='diffSCESets.html'>diffSCESets</a></code></p></td>
+      <td><p>Output from <code><a href='diffSCEs.html'>diffSCEs</a></code></p></td>
     </tr>
     </table>
     
@@ -124,22 +124,22 @@ Error (RMSE) for the various properties and ranks them.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
 <span class='no'>summary</span> <span class='kw'>&lt;-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
 <span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#&gt;   Dataset Statistic          MAD MADScaled MADRank          MAE MAEScaled
-#&gt; 1   Splat      Mean     2.680705       NaN       1     2.613714       NaN
-#&gt; 2   Splat  Variance    11.803596       NaN       1    10.839966       NaN
-#&gt; 3   Splat ZerosGene    35.000000       NaN       1    41.705000       NaN
-#&gt; 4   Splat   MeanVar    11.293733       NaN       1    12.494680       NaN
-#&gt; 5   Splat MeanZeros    45.000000       NaN       1    43.895000       NaN
-#&gt; 6   Splat   LibSize 62080.000000       NaN       1 63692.450000       NaN
-#&gt;   MAERank         RMSE RMSEScaled RMSERank
-#&gt; 1       1     3.125188        NaN        1
-#&gt; 2       1    13.638865        NaN        1
-#&gt; 3       1    45.945892        NaN        1
-#&gt; 4       1    15.583460        NaN        1
-#&gt; 5       1    53.301735        NaN        1
-#&gt; 6       1 64680.944707        NaN        1</div></pre>
+#&gt; 1   Splat      Mean     2.402442       NaN       1     2.481297       NaN
+#&gt; 2   Splat  Variance    11.598939       NaN       1    10.337802       NaN
+#&gt; 3   Splat ZerosGene    35.000000       NaN       1    41.345000       NaN
+#&gt; 4   Splat   MeanVar    11.259905       NaN       1    12.078602       NaN
+#&gt; 5   Splat MeanZeros    40.000000       NaN       1    41.945000       NaN
+#&gt; 6   Splat   LibSize 59020.500000       NaN       1 59926.850000       NaN
+#&gt;   MAERank        RMSE RMSEScaled RMSERank
+#&gt; 1       1     3.03372        NaN        1
+#&gt; 2       1    13.03590        NaN        1
+#&gt; 3       1    45.66043        NaN        1
+#&gt; 4       1    15.08035        NaN        1
+#&gt; 5       1    51.61323        NaN        1
+#&gt; 6       1 61634.63305        NaN        1</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>