Question: use differences in expression as input for co-expression network?
0
gravatar for Lin
8 weeks ago by
Lin50
Lin50 wrote:

Hi all,

if I have expression data from two time-points and I am interested in changes over time- Would it be possible to use the difference in expression between the time-points (delta values) as input for WGCNA (or for co-expression networks in general)?

I am not sure if there could be a problem with the assumptions (for example scale-free connectivity etc.). And I think the interpretation would become more complicated, and probably an unsigned network would make more sense than a signed one?

Thanks for any suggestions!

wgcna co-expression • 109 views
ADD COMMENTlink modified 6 weeks ago by mikhael.manurung170 • written 8 weeks ago by Lin50
Answer: use differences in expression as input for co-expression network?
0
gravatar for mikhael.manurung
6 weeks ago by
Netherlands
mikhael.manurung170 wrote:

Hi Lin,

It is possible and it has been done before, for example see this this paper .

So you can log-transform your data (if your data is an RNA-Seq data) and then: countmat2 - countmat1. This will give you 'fold change' expression matrix relative to the baseline.

ADD COMMENTlink written 6 weeks ago by mikhael.manurung170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour