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Question: Extracting normalized count data from DESeq2
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gravatar for banerjee.deblina
10 days 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

ADD COMMENTlink modified 10 days ago by Michael Love19k • written 10 days ago by banerjee.deblina0
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gravatar for Michael Love
10 days ago by
Michael Love19k
United States
Michael Love19k 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 10 days ago by Michael Love19k

In particular this code:

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

ADD REPLYlink modified 10 days ago • written 10 days ago by Michael Love19k

Thanks for the reply. I some how missed that.

 

ADD REPLYlink written 10 days ago by banerjee.deblina0
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