Question: Extracting normalized count data from DESeq2
0
gravatar for banerjee.deblina
13 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 • 152 views
ADD COMMENTlink modified 13 months ago by Michael Love25k • written 13 months ago by banerjee.deblina0
Answer: Extracting normalized count data from DESeq2
0
gravatar for Michael Love
13 months ago by
Michael Love25k
United States
Michael Love25k 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 13 months ago by Michael Love25k

In particular this code:

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

ADD REPLYlink modified 13 months ago • written 13 months ago by Michael Love25k

Thanks for the reply. I some how missed that.

 

ADD REPLYlink written 13 months ago by banerjee.deblina0
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