Use rlog transformation.

DavyCats · Oct 11, 2017 · b9bed40 · b9bed40
1 parent 17bfb62
commit b9bed40
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/plot-pca.R b/scripts/plot-pca.R
@@ -6,7 +6,7 @@ library("DESeq2")
 dds <- readRDS(snakemake@input[[1]])
 
 # obtain normalized counts
-counts <- counts(dds, normalized=TRUE)
+counts <- rlog(dds, blind=FALSE)
 svg(snakemake@output[[1]])
 plotPCA(counts, intgroup=snakemake@params[["pca_labels"]])
 dev.off()