WGCNA Co-expression network analysis on cuffdiff output
0
1
Entering edit mode
5.8 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 • 1.7k views
ADD COMMENT
0
Entering edit mode

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 - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.

ADD REPLY
0
Entering edit mode

I have used Cuffdiff after STAR.

ADD REPLY
0
Entering edit mode

What have you tried to solve your WGCNA question?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 3951 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6