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Question: Extracting normalized count data from DESeq2
0
gravatar for banerjee.deblina
5 months ago by
banerjee.deblina0 wrote:

Hi Michael,

I am using DESeq2 to do differential analysis for my RNAseq data. I gave raw read count as input and was successful in getting the results. But I want to extract the intermediate normalized file, for making a heatmap. How can I extract that?

Thanks

Deblina

deseq2 • 99 views
ADD COMMENTlink modified 5 months ago by Michael Love21k • written 5 months ago by banerjee.deblina0
Answer: Extracting normalized count data from DESeq2
0
gravatar for Michael Love
5 months ago by
Michael Love21k
United States
Michael Love21k wrote:

Take a look at the documentation. Nearly any basic question is answered there. For this one see ?counts and the arguments. Also the vignette shows how to get normalized counts.

ADD COMMENTlink written 5 months ago by Michael Love21k

In particular this code:

http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#heatmap-of-the-count-matrix

ADD REPLYlink modified 5 months ago • written 5 months ago by Michael Love21k

Thanks for the reply. I some how missed that.

 

ADD REPLYlink written 5 months ago by banerjee.deblina0
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