How to extract the read counts after normalization with DESeq in R?

Question

[Amr]

I have done the normalization with deseq2 in R, please how can extract csv file for the normalized counts as I want to extract columns of some cell lines to perform GSEA?

dds <- DESeq(dds)

res <- results(dds)

Thanks in advance

Answer 1

[Marco Pannone]

count_data <- counts(dds, normalized=TRUE)
write.csv(as.data.frame(count_data),file="count_data.csv")

Naturally, if you are interested only in some samples (columns), then you need to add one more line of code to subset the dataframe accordingly to your aim.

[Amr]

Thank you so much it worked :)