From 0df208070b6aa8f7ce4a56be08bb6b7e8155f40a Mon Sep 17 00:00:00 2001
From: Davis McCarthy <davismcc@gmail.com>
Date: Wed, 2 Oct 2019 00:04:54 +1000
Subject: [PATCH] Bug fix for exprs-norm-reads
---
course_files/exprs-norm-reads.Rmd | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/course_files/exprs-norm-reads.Rmd b/course_files/exprs-norm-reads.Rmd
index ac95675..070d805 100644
--- a/course_files/exprs-norm-reads.Rmd
+++ b/course_files/exprs-norm-reads.Rmd
@@ -135,7 +135,7 @@ plotRLE(
-```{r}
+```{r, eval=FALSE}
reads.qc <- getBMFeatureAnnos(
reads.qc,
filters = "ensembl_gene_id",
@@ -152,20 +152,20 @@ reads.qc <- getBMFeatureAnnos(
)
```
-```{r}
+```{r, eval=FALSE}
reads.qc.ann <- reads.qc[!is.na(rowData(reads.qc)$ensembl_gene_id), ]
```
-```{r}
+```{r, eval=FALSE}
eff_length <-
abs(rowData(reads.qc.ann)$end_position - rowData(reads.qc.ann)$start_position) / 1000
```
-```{r}
+```{r, eval=FALSE}
tpm(reads.qc.ann) <- log2(calculateTPM(reads.qc.ann, eff_length) + 1)
```
-```{r norm-pca-tpm-reads, fig.cap = "PCA plot of the tung data after TPM normalisation"}
+```{r norm-pca-tpm-reads, eval=FALSE, fig.cap = "PCA plot of the tung data after TPM normalisation"}
tmp <- runPCA(
reads.qc.ann,
exprs_values = "tpm",
@@ -178,11 +178,11 @@ plotPCA(
)
```
-```{r}
+```{r, eval=FALSE}
tpm(reads.qc.ann) <- log2(calculateFPKM(reads.qc.ann, eff_length) + 1)
```
-```{r norm-pca-fpkm-reads, fig.cap = "PCA plot of the tung data after FPKM normalisation", eval=FALSE}
+```{r norm-pca-fpkm-reads, eval=FALSE, fig.cap = "PCA plot of the tung data after FPKM normalisation", eval=FALSE}
tmp <- runPCA(
reads.qc.ann,
exprs_values = "tpm",
--
GitLab