problem with WGCNA
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@nazaninhoseinkhan-9194
Last seen 8.3 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 • 1.8k views
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@peter-langfelder-4469
Last seen 28 days 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
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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

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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.
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