As described previously here: https://support.bioconductor.org/p/66067/ The way to access the normalized count table in DESeq2 can be done by the following script lines: dds <- estimateSizeFactors(dds) counts(dds, normalized=TRUE)

I'm trying to understand if the normalized count table that can extracted using the above is taking into consideration a batch effect that is modeled in the design of DESeq2.

For example if I have a batch in my design: design = ~ condition + Batch 1. Is the table accessed normalized for the batch? 2. If so, is there a way to get two separate count tables: a. normalized without batch. b. normalized with batch. 3. If not, is there a way to normalize for the batch and access it using the basic functions or arguments in DESEq2.

Thanks

No, size factors dont use the design.

In order to get data corrected for batch, we recommend VST followed by removal of the batch effect with a linear regression, see the FAQ in the vignette.