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?