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

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