Consensus module detection using WGCNA

Question

[Nitin]

Hello,

I recently started to work on consensus modules identification using WGCNA (R package). I went through tutorials related to this in WGCNA website In these tutorials authors had mentioned constructed female liver and male liver datasets. When I looked into input data regarding female and liver data sets I found that they both have same number of genes (3600) each ofcourse different expression values. Now my question is if we use different datasets as followes

Data1 : 700 genes

Data2: 300 genes

Is it possible to compared these datasets and construct consensus modules using WGCNA or not. Because when I tried using my datasets with different number of genes it gave following error

exprSize = checkSets(multiExpr)
Error in checkSets(multiExpr) : 
  Incompatible number of genes in set 1 and 2

Does this mean should I consider only common genes between datasets to construct consensus modules?

Let me know.

Thanks and Regards,
Sai

[tothepoint]

I am having the same problem..Please let me know if you have the solution.

Answer 1

[ali.hassan.nehme]

You should identify the common genes between the two data sets and use them to do the consensus module analysis.