Bug fix for exprs-norm-reads

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",