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Question: WGCNA Co-expression network analysis on cuffdiff output
1
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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!

ADD COMMENTlink 17 months ago sbb • 10
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What have you tried? - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.

ADD REPLYlink 17 months ago
andrew.j.skelton73
5.7k
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I have used Cuffdiff after STAR.

ADD REPLYlink 17 months ago
sbb
• 10
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What have you tried to solve your WGCNA question?

ADD REPLYlink 17 months ago
andrew.j.skelton73
5.7k
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Cross-posted on Bioconductor: https://support.bioconductor.org/p/113105/

ADD REPLYlink 17 months ago
Kevin Blighe
43k
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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 fdor your statistically significant genes from CuffDiff.
ADD REPLYlink 17 months ago
Kevin Blighe
43k

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