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WGCNA Co-expression network analysis on cuffdiff output

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!

wgcna cuffdiff
• 2,402 views • link
updated by Ram Ram • written by sbb • sbb

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 - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

I have used Cuffdiff after STAR.

• 1 views • link
written by sbb • sbb

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.
• 1 views • link
written by Kevin Blighe Kevin Blighe

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