Hi everybody,

I recently changed from DESeq to DESeq2 to perform my RNA-Seq analysis.

I would like to know how I could include the baseMean values for the two conditions I am using (as it was automatically done in DESeq).

This is how I performed part of it:

#Differential expression analysis dds <- DESeq(dds) res <- results(dds, cooksCutoff=FALSE) res <- res[order(res$padj),] sizeFactors(dds) head (counts (dds)) head (counts(dds, normalized=TRUE))

head(res)

mcols(res, use.names=TRUE)

dds=estimateDispersions (dds) plotDispEsts( dds )

dds<- DESeq(dds)

#to export table write.csv(as.data.frame(res), file.choose())

Thanks, if you need any other info tell me ;)

While the site search isn't so great, you can use Google to find similar posts. If I punch in this into Google:

site:https://support.bioconductor.org/ deseq2 basemean each condition

The top post gives some code to accomplish this. (it's thread 63567)