Commit 0df20807 authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Bug fix for exprs-norm-reads

parent 835ad35d
Pipeline #944 passed with stage
in 4 seconds
......@@ -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",
......
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