diff --git a/DESCRIPTION b/DESCRIPTION
index 1bc88388b9cc8af574a8901503c954276d0b1aa8..60ea856fc6ebae2b79300e144cb6918d69c2408b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.0.0
-Date: 2017-04-23
+Version: 1.0.1
+Date: 2017-04-28
 Author: Luke Zappia
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index dd555cb84324f931ed635f485d5edae3668a6eef..83e091a7bacd5c5b207e74dd37f2e08eb3a1502e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+# 1.0.1
+
+* Fix scales in some difference plots
+* Fix colours in difference plots
+* Fix panel legends
+
+# 1.0.0
+
+* Bioconductor 3.5 release
+
 # 0.99.15
 
 * Add summariseDiff function
diff --git a/R/compare.R b/R/compare.R
index c11f53af2dec964b4a7d828bb241b71a4176a002..07b09a64578db28796d8f06462aeef0f80085ded 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -271,6 +271,8 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
 
     if (!(ref %in% names(sces))) {
         stop("'ref' must be the name of an SCESet in 'sces'")
+    } else {
+        ref.idx <- which(names(sces) == ref)
     }
 
     if (!is.null(colours)) {
@@ -278,6 +280,7 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                    len = length(sces) - 1)
     } else {
         colours <- scales::hue_pal()(length(sces))
+        colours <- colours[-ref.idx]
     }
 
     ref.dim <- dim(sces[[ref]])
@@ -400,7 +403,6 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                 colour = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_boxplot() +
-        scale_y_continuous(limits = c(0, 100)) +
         scale_colour_manual(values = colours) +
         ylab(paste("Rank difference percentage zeros")) +
         ggtitle("Difference in zeros per gene") +
@@ -411,7 +413,6 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
                                 colour = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_boxplot() +
-        scale_y_continuous(limits = c(0, 100)) +
         scale_colour_manual(values = colours) +
         ylab(paste("Rank difference percentage zeros")) +
         ggtitle("Difference in zeros per cell") +
@@ -559,7 +560,7 @@ makeCompPanel <- function(comp, title = "Comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p3 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +
@@ -644,7 +645,7 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p5 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +
@@ -743,7 +744,7 @@ makeOverallPanel <- function(comp, diff, title = "Overall comparison",
         plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
     }
 
-    plots$leg <- cowplot::get_legend(plots$p1 +
+    plots$leg <- cowplot::get_legend(plots$p7 +
                                          theme(legend.position = "bottom"))
 
     panel <- cowplot::ggdraw() +
diff --git a/README.md b/README.md
index 9f52c1d4a06edd89112669116ebd03b94cb9d30f..eb68a0acd2965ad82da78c2fef3bab1ae1f5ef8f 100644
--- a/README.md
+++ b/README.md
@@ -14,15 +14,15 @@ data. Splatter provides a common interface to multiple simulations that have:
 * Functions for simulating counts using those parameters
 
 Splatter is built on top of [`scater`][scater] and stores simulations in
-`SCESet` objects.
+`SCESet` objects. Splatter also has functions for comparing simulations and real
+datasets.
 
 ## Installation.
 
 ### Development version
 
-Splatter has been accepted into the development version of [Bioconductor][bioc]
-and hence requires the development version of R (>=3.4) and the development
-version of Bioconductor (3.5).
+Splatter has been accepted into the latest version of [Bioconductor][bioc]
+and hence requires the latest version of R (>=3.4).
 
 If you have these installed Splatter can be installed from Bioconductor using
 `biocLite`:
@@ -43,13 +43,6 @@ aren't required for core functionality). Building the vignette may sometimes
 fail when run from the command line, if this happens try running the install
 command in RStudio.
 
-### Release version
-
-The last version of Splatter that is compatible with the current version of
-R (3.3) is v0.99.0 which can be downloaded [here][rel33]. There are no
-significant changes to functionality and this version should be fine for most
-users until the next R/Bioconductor release (in approximately April 2017).
-
 ## Getting started
 
 Once installed the best place to get started is the vignette. For most users
@@ -69,4 +62,4 @@ This is a detailed document that introduces the main features of Splatter.
 [contrib]: https://github.com/Bioconductor/Contributions/issues/209
 [bioc]: https://bioconductor.org/packages/devel/bioc/html/splatter.html
 [vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
-[rel33]: https://github.com/Oshlack/splatter/releases/tag/v0.99.0
+