Hello,

I'm processing RNA-seq data (sampleA, sampleB) with featureCounts, and DE analysis with DESeq2. In the DESeq2 output, there are only baseMean, log2FoldChange...

I would like to extract the expected counts calculated by DESeq2 (already normalized, not the raw read counts from featureCounts).

Is there anyone knowing how to extract the expected counts value for each sample?

For example, geneID sampleA sampleB GeneA 5.666 4.333 GeneB 4.444 3.222 GeneC 4.111 7.555 . . .

Thanks in advance.

Edward

DESeq2 operates on raw counts. It doesn’t use normalized counts internally. You can generate counts / size factors, see the vignette and ?counts

counts(dds, normalized = TRUE)