I have a question regarding normalized counts of DESeq2 (Not VST or rlog transformed).
I used counts(normalized=TRUE) to get normalized data after DESeq() as follows.
norm_tbl <- counts(dds, normalized=TRUE)
My question is that:
1. Can this normalized count table be used for downstream analysis, which I plan to use normalized count as dependent variable in modelling? Do this normalization account for normalizing for sequence depth variance?
2. Is this normalization affected by design formula when I created the DESeq dataset? I tried several different formulas, but no change can be observed for normalized counts.
Thanks for helping in advance.