Hello,

In a multi-factor DESeq2 design, I want to extract normalized counts adjusted by multi-factor designs; batch, gender, etc...

But counts(dds, normalized = TRUE) only accounts for size factor.

A similar post was made 7 years ago, but at that time it stated that DESeq2 did not have such a feature. Extracting normalized DESeq2 counts for a multi-factor design?

Is it still impossible to access the counts which have been normalized for multi-factor designs and size factor?

Thanks.

It's still not possible directly in DESeq2 as DESeq2 internally adds the covariates into its model rather than ever directly altering counts. Your options are tools like Combat, ComBat-Seq or the removeBatchEffect function from limma to regress factors from the counts.