From cbb7c1d7a354d8e413efc2367509a521b4b096fc Mon Sep 17 00:00:00 2001
From: Davis McCarthy <dmccarthy@svi.edu.au>
Date: Tue, 1 Oct 2019 19:19:02 +1000
Subject: [PATCH] Bug fix in exprs-norm

---
 course_files/exprs-norm.Rmd | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/course_files/exprs-norm.Rmd b/course_files/exprs-norm.Rmd
index c4df548..dd8614f 100644
--- a/course_files/exprs-norm.Rmd
+++ b/course_files/exprs-norm.Rmd
@@ -541,7 +541,7 @@ instead of transcripts. `scater` uses the
 [biomaRt](https://bioconductor.org/packages/release/bioc/html/biomaRt.html)
 package, which allows one to annotate genes by other attributes:
 
-```{r, message = FALSE, warning = FALSE}
+```{r, message = FALSE, warning = FALSE, eval=FALSE}
 umi.qc <- getBMFeatureAnnos(
     umi.qc,
     filters = "ensembl_gene_id", 
@@ -579,19 +579,19 @@ umi.qc <- getBMFeatureAnnos(
 
 Some of the genes were not annotated, therefore we filter them out:
 
-```{r}
+```{r, eval=FALSE}
 umi.qc.ann <- umi.qc[!is.na(rowData(umi.qc)$ensembl_gene_id), ]
 ```
 
 Now we compute the total gene length in Kilobases by using the `end_position`
 and `start_position` fields:
 
-```{r}
+```{r, eval=FALSE}
 eff_length <- 
     abs(rowData(umi.qc.ann)$end_position - rowData(umi.qc.ann)$start_position) / 1000
 ```
 
-```{r length-vs-mean, fig.cap = "Gene length vs Mean Expression for the raw data"}
+```{r length-vs-mean, eval=FALSE, fig.cap = "Gene length vs Mean Expression for the raw data"}
 plot(eff_length, rowMeans(counts(umi.qc.ann)))
 ```
 
@@ -608,12 +608,12 @@ page](https://www.biostars.org/p/83901/).
 
 Now we are ready to perform the normalisations:
 
-```{r}
+```{r, eval=FALSE}
 tpm(umi.qc.ann) <- log2(calculateTPM(umi.qc.ann, eff_length) + 1)
 ```
 
 Plot the results as a PCA plot:
-```{r norm-pca-fpkm, fig.cap = "PCA plot of the tung data after TPM normalisation"}
+```{r norm-pca-fpkm, eval=FALSE, fig.cap = "PCA plot of the tung data after TPM normalisation"}
 tmp <- runPCA(
   umi.qc.ann,
   exprs_values = "tpm",
@@ -626,11 +626,11 @@ plotPCA(
 )
 ```
 
-```{r}
+```{r, eval=FALSE}
 tpm(umi.qc.ann) <- log2(calculateFPKM(umi.qc.ann, eff_length) + 1)
 ```
 
-```{r norm-pca-tpm, fig.cap = "PCA plot of the tung data after FPKM normalisation"}
+```{r norm-pca-tpm, eval=FALSE, fig.cap = "PCA plot of the tung data after FPKM normalisation"}
 tmp <- runPCA(
   umi.qc.ann,
   exprs_values = "tpm",
-- 
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