I have a conceptual question about the counts() function in DESeq2.
counts() uses a DESeq2 object as an input (usually called as dds). While creating this object, we can add covariates to the design formula. Let's say the formula is ~ genotype + age.
Does counts() generate normalized counts values corrected for covariates, or NOT considering the covariates?
dds <- DESeqDataSetFromMatrix(countData = counts_mat, colData = samples, design = ~ genotype + age) dds <- DESeq(dds, parallel = T) counts(dds)