Question: WGCNA Co-expression network analysis on cuffdiff output
1
gravatar for sbb
16 months ago by
sbb10
Germany
sbb10 wrote:

Hello,

I am struggling with running WGCNA on cuffdiff output consisting of 28 pairwise comparisons (Time series Analysis). Can someone suggest way out to perform WGCNA for each comparisons separately.

Thanks!

cuffdiff forum wgcna • 552 views
ADD COMMENTlink modified 15 months ago • written 16 months ago by sbb10

What have you tried? - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.

ADD REPLYlink written 16 months ago by andrew.j.skelton735.9k

I have used Cuffdiff after STAR.

ADD REPLYlink written 16 months ago by sbb10

What have you tried to solve your WGCNA question?

ADD REPLYlink written 16 months ago by andrew.j.skelton735.9k

Cross-posted on Bioconductor: https://support.bioconductor.org/p/113105/

ADD REPLYlink written 16 months ago by Kevin Blighe53k

The WGCNA developer replied to you on Bioconductor but never followed-up.

You have 2 options:

  1. perform WGCNA on your entire [unfiltered] dataset
  2. perform WGCNA on your filtered dataset, i.e., filtered for your statistically significant genes from CuffDiff.
ADD REPLYlink modified 4 months ago • written 15 months ago by Kevin Blighe53k
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