Question: use differences in expression as input for co-expression network?
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gravatar for Lin
4 months 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 • 144 views
ADD COMMENTlink modified 3 months ago by mikhael.manurung200 • written 4 months ago by Lin50
Answer: use differences in expression as input for co-expression network?
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gravatar for mikhael.manurung
3 months ago by
Netherlands
mikhael.manurung200 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 3 months ago by mikhael.manurung200
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