Question: Get normalized count Data using DESeq2 in R
gravatar for Krish Srinivasan
3.4 years ago by
Krish Srinivasan20 wrote:

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.


rna-seq R • 6.8k views
ADD COMMENTlink modified 3.4 years ago by Sentinel156130 • written 3.4 years ago by Krish Srinivasan20
gravatar for WouterDeCoster
3.4 years ago by
WouterDeCoster43k wrote:

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).

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by WouterDeCoster43k
gravatar for Sentinel156
3.4 years ago by
Melbourne, Australia
Sentinel156130 wrote:

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

ADD COMMENTlink written 3.4 years ago by Sentinel156130
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