Dear group, I have code that creates a LumiBatch object from two matrices of data: lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD ) This code refuses to work in R 2.9: Error in `sampleNames<-`(`*tmp*`, value = character(0)) : 'value' length (0) must equal sample number in AssayData (0) And I am unable to trace the source of the error. I've also tried setting up phenoData and featureData objects, to no avail. FYI, the following call works fine: lumiBatch <- new( "ExpressionSet", exprs = signalRaw, se.exprs = beadSD ) How can I fix this problem? And this is my session info: R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETAR Y=English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.10.2 RSQLite_0.7-2 DBI_0.2-4 preprocessCore_1.6.0 mgcv_1.5-5 affy_1.22.1 [7] annotate_1.22.0 AnnotationDbi_1.6.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 grid_2.9.2 lattice_0.17-25 nlme_3.1-93 tools_2.9.2 xtable_1.5-5 Best, Michal

Hi Michal I just checked the code and figured out the problem. The reason is that Biobase made some changes recently, but I didn't modify my code accordingly. Now I have fixed the problem in the lumi Release version (1.12.1) and developing version (1.13.1). I may take several days before it is available. Also you need to updated your R to 2.10.0 if you install the lumi package using biocLite(). Thanks for reporting the problem. Pan On 11/5/09 1:20 PM, "Gilbert Feng" <g-feng at="" northwestern.edu=""> wrote: > From: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > Organization: Genome Quebec > Reply-To: Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> > Date: Tue, 3 Nov 2009 12:15:39 -0500 > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Constructing a LumiBatch manually > > Dear group, > > I have code that creates a LumiBatch object from two matrices of data: > > lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD ) > > This code refuses to work in R 2.9: > > Error in `sampleNames<-`(`*tmp*`, value = character(0)) : > 'value' length (0) must equal sample number in AssayData (0) > > And I am unable to trace the source of the error. > I've also tried setting up phenoData and featureData objects, to no avail. > > FYI, the following call works fine: > lumiBatch <- new( "ExpressionSet", exprs = signalRaw, se.exprs = beadSD ) > > How can I fix this problem? > > And this is my session info: > > R version 2.9.2 (2009-08-24) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONET ARY=Engl > ish_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_1.10.2 RSQLite_0.7-2 DBI_0.2-4 > preprocessCore_1.6.0 mgcv_1.5-5 affy_1.22.1 > [7] annotate_1.22.0 AnnotationDbi_1.6.1 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 grid_2.9.2 lattice_0.17-25 nlme_3.1-93 > tools_2.9.2 xtable_1.5-5 > > Best, > Michal