Peter, Thank you. In fact, I am also very interesting to WGCNA.
On Sat, Jun 16, 2012 at 3:29 AM, Peter Langfelder <peter.langfel...@gmail.com> wrote: > On Fri, Jun 15, 2012 at 8:04 AM, Ingezz <irholt...@gmail.com> wrote: >> 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? > > Hi Inge, > > first, I suggest that in the future you contact me directly, since > others on this list probably have no idea what we're talking about. > > It is difficult to diagnose the problem without the data. I suggest > you specify the verbose argument to both functions with a high value > (e.g., 5) which should produce more informative output. > > I assume you are aware of the fact that the function goodSamplesGenes > returns a list whose component allOK determines whether any genes or > samples should be removed. Other components in the list specify which > genes and/or samples should be removed. The actual removal needs to be > done by you (I haven't written a function to do that yet but may do so > in the future to make it more convenient). In this sense the error > message is a bit misleading and I will change that as well. > > HTH, > > Peter > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
