Question

problem with WGCNA

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nazaninhoseinkhan • 0

@nazaninhoseinkhan-9194

Last seen 8.9 years ago

Dear all,

I am working with WGCNA package on a bacterial species. Everything seems OK, but when I checked the co-expression of 4 genes (belong to a locus) that already known to be co-transcribed, only 2 of them were placed in the same module and the two others were in two different module.

I can not understand the reason.

I want to know if I can rely on WGCNA for the remaining cases or not.

I also want to know the reasons for observing such cases

I will appreciate any help

Nazanin

geneexpression • 2.1k views

ADD COMMENT • link updated 9.1 years ago by Peter Langfelder ★ 3.0k • written 9.1 years ago by nazaninhoseinkhan • 0

Martin Morgan · Answer 1 · 2015-11-15

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Peter Langfelder ★ 3.0k

@peter-langfelder-4469

Last seen 5 weeks ago

United States

Well, it's difficult to say what is going on without seeing the data. However, one thing you can do is to check the correlations among the 4 genes in your data. Create a matrix of the expression of the 4 genes and use cor() on them to see whether they are really co-expressed in your data. If they are strongly co-expressed, it could be that you need to make the module identification a bit more conservative (lower deepSplit argument). There could be other issues as well, but you can start with these two suggesstions. Peter

ADD COMMENT • link updated 9.1 years ago by Martin Morgan 25k • written 9.1 years ago by Peter Langfelder ★ 3.0k

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Dear Peter,

First of all thank you for the comments.

I computed the correlation among four genes. The correlations between gene A,B,C and D was as follow:

0.971778	D-C
-0.5559	C-B
-0.19767	B-A
-0.56853	D-B
0.326305	D-A
0.37033	C-A

I had included 252 samples( heterogeneous conditions). Do you think those negative correlations or low positive correlations are due to the heterogeneity in samples conditions.

Another questions is how I can argue the observed results in my paper. In the previous works it has been frequently been indicated that these 4 genes are co-transcribed, because they are in the same locus.

Regards

Nazanin

ADD REPLY • link 9.1 years ago nazaninhoseinkhan • 0

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Well, the correlations answer your question why the genes ended up in different modules, presumably except for D and C which would obviously end up in the same module. Sorry, I cannot help you with the data interpretation or troubleshooting.

ADD REPLY • link updated 9.1 years ago by Martin Morgan 25k • written 9.1 years ago by Peter Langfelder ★ 3.0k