Entering edit mode
16 months ago
synat.keam ▴ 70
Sorry for another post. I have RNAseq data and used DESeq2 pipeline for differntially expressed genes. Now I am doing WGCNA and the author suggest to filter genes based on mean expression rather than variance. I am wondering whether anyone has ever filtered genes based on mean expression and could suggest some code chunks.
If you need only exp values based on mean use cufflinks.
I'm not sure whether DESeq2 filter genes based on mean expression.
Kashiff, I will try your suggestion. Thank for you both of you for taking time to respond.
Hey! DESeq2 does not filter genes with low read counts across samples by default, but you need to perform such filtering step, simple as this:
You mean filtering genes with very low read counts as also suggested in the DESeq2 pipeline?