Question: DESeq2 rlog as the input for ARACNE
0
gravatar for Tom
12 weeks ago by
Tom10
Tom10 wrote:

Dear all,

I have been using DESeq2 for RNA sequencing-based gene expression analysis, and recently trying to use ARACNe for regulatory network inference.

Are rlog values appropriate as the input for ARACNe analysis?

Considering that rlog does not normalize expression values by gene lengths, should I simply use RPKM/FPKM values for that kind of analysis?

Thanks, Tom

deseq2 • 67 views
ADD COMMENTlink modified 12 weeks ago by Michael Love26k • written 12 weeks ago by Tom10
Answer: DESeq2 rlog as the input for ARACNE
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gravatar for Michael Love
12 weeks ago by
Michael Love26k
United States
Michael Love26k wrote:

Can you describe what the qualities of input data are required?

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Michael Love26k

Edited: that should have said “qualities”

ADD REPLYlink written 12 weeks ago by Michael Love26k
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