Search
Question: Extracting normalized count data from DESeq2
0
gravatar for banerjee.deblina
9 weeks 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 9 weeks ago by Michael Love20k • written 9 weeks ago by banerjee.deblina0
0
gravatar for Michael Love
9 weeks ago by
Michael Love20k
United States
Michael Love20k 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 9 weeks ago by Michael Love20k

In particular this code:

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

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Michael Love20k

Thanks for the reply. I some how missed that.

 

ADD REPLYlink written 9 weeks ago by banerjee.deblina0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 161 users visited in the last hour