Question

Extracting normalized count data from DESeq2

0

Entering edit mode

banerjee.deblina • 0

@banerjeedeblina-17330

Last seen 5.7 years ago

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 • 409 views

ADD COMMENT • link updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by banerjee.deblina • 0

score 0 · Answer 1 · 2018-09-13

0

Entering edit mode

Michael Love 42k

@mikelove

Last seen 2 hours ago

United States

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 COMMENT • link 5.7 years ago Michael Love 42k

0

Entering edit mode

In particular this code:

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