Get normalized count Data using DESeq2 in R

Question

[Krish Srinivasan]

Hello everyone,

I have 54 HT-seq Count files from an old experiment that I am reanalyzing. They are composed of combinations of the 2 treatment groups (Wildtype and Treatment), 3 exposures (water, tBOOH, diquat), and 3 times points. I need to create a matrix of the normalized count data for each gene in each sample. I am not sure how to start, any help would be appreciated.

Thanks,

Answer 1

[WouterDeCoster]

What you are looking for is extraction of counts after variance stabilizing transformation (vsd/vst) or rlog normalization. You can find both described clearly in the DESeq2 manual (2.1.2 Extracting transformed values).

Answer 2

[Sentinel156]

Hi, this is pretty simple using DESeq2's counts function and has been asked many times before. See here and here for examples.