>Dear Antti, > >Thanks for your reply to the Earlier question. I have managed to run the >GPLearn command and obtained some interesting results. > >However, when I try to run the GPRanktargets command I get this error >"Error in yvar + sigma : non-conformable arrays". > >I think this means that my Data lacks calculated variances. As I >understand from your User guide you process affymetrix Datasets using the >mmgmos command from the PUMA package which automatically calculates the >variances for you. However, when I try to run my expression value matrix >through this mmgmos command it doesn't work and gives me this error >"unable to find an inherited method for function ?probeNames? for >signature ?"ExpressionTimeSeries"? > >Please advise on whether I should use an independent method to calculate >the variances so the GPRanktargets works or whether the error lies >somewhere else. > >Thanks >Anisha > > > > > > > >On 06/02/2014 06:32, "Antti Honkela" <antti.honkela at="" hiit.fi=""> wrote: > >>Dear Anisha, >> >>GPLearn function expects the data (your MyExpressionSet) to be an >>ExpressionTimeSeries object that you can create using functions >>processData() or processRawData(). Can you please make sure you are >>passing it the correct kind of object, as a wrong kind of object could >>cause an error like you describe? >> >>Furthermore, in your example you specify a model with a regulating TF >>but no targets. You should add some targets to get a sensible model. For >>screening candidate targets GPRankTargets() provides an easier option >>than GPLearn(). >> >>Thanks a lot for your report, I will update the package to make the >>error message more informative! >> >> >>Antti >> >> >>On 2014-02-05 21:47 , Solanki, Anisha wrote: >>> >>> When I tried to run the GPLearn command with my expression set it gives >>>me an error >>> >>> model <- GPLearn(MyExpressionSet, TF="ENSMUSG00000001300", >>>useGpdisim=TRUE, quiet=TRUE) >>> >>> "Error in yvar[[1]] :subscript out of bounds". >>> >>> Please advise >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>>http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >>-- >>Antti Honkela >>antti.honkela at hiit.fi - http://www.hiit.fi/u/ahonkela/ >> >