WGCNA Co-expression network analysis on cuffdiff output

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5.6 years ago

sbb ▴ 10

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 • 1.6k views

ADD COMMENT • link updated 11 months ago by Ram 43k • written 5.6 years ago by sbb ▴ 10

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 - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.

ADD REPLY • link 5.6 years ago by andrew.j.skelton73 6.5k

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I have used Cuffdiff after STAR.

ADD REPLY • link 5.6 years ago by sbb ▴ 10

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What have you tried to solve your WGCNA question?

ADD REPLY • link 5.6 years ago by andrew.j.skelton73 6.5k

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

ADD REPLY • link 5.6 years ago by Kevin Blighe 87k

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

You have 2 options:

perform WGCNA on your entire [unfiltered] dataset
perform WGCNA on your filtered dataset, i.e., filtered for your statistically significant genes from CuffDiff.

ADD REPLY • link 4.6 years ago by Kevin Blighe 87k

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