By calling DESeq() on a DESeqDataset it estimates the size factors (normalization) automatically. How can I access this data? I must be stored somewhere. I would like to access the normalized counts.
>dds <- DESeq()
estimating size factors
gene-wise dispersion estimates
I know there is the counts() function but why use this if the calculation is already done?
## S4 method for signature 'DESeqDataSet'
counts(object, normalized = FALSE)
Does anybody have any hints?