[R] wgcna

[Ingezz]

Dear Peter,

I am trying to apply the WGCNA meta-analysis for two (or more) microarray
datasets-tutorial to my own data. 

> mp=modulePreservation(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType="signed", 
> nPermutations=30,maxGoldModuleSize=100,maxModuleSize=400)

However, the error I am getting is: 

Error in .checkExpr(multiData, verbose, indent) : 
  The submitted 'multiExpr' data contain genes or samples
   with zero variance or excessive counts of missing entries.
   Please use the function goodSamplesGenes on each set to filter out the
problematic
   genes and samples before running modulePreservation.

Seems pretty clear, but applying goodSamplesGenes function results in no
exclusions for both arrays. 

>  GM2 <- goodSamplesGenes(M2, minFraction = 1/2, minNSamples =8, minNGenes
> =20) 

What could be the issue here? Should I increase the stringency? What
stringency should be used with goodsamplegenes for modulepreservation to
work? 

Many thanks in advance! 

Kind regards,
Inge 

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