Hi,

From a Deseq2 analysis, I have just the final table of results (I guess res(dds)). My first question is if the counts there are normalized counts or just the counts for each gene from the initial data without any transformation? My second question is if I can do with just with these data outlier analysis at this stage, as I don't have the dds object?

Thanks in advance !

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You can get normalised count from Deseq2

normcounts <- counts(dds, normalized = TRUE)
write.csv(normcounts file="normcounts.csv")