Hi Paolo Please update your R and lumi package. I remember this was fixed a while ago. Pan > Date: Tue, 13 Mar 2012 15:39:43 +0100 > From: Paolo Kunderfranco <paolo.kunderfranco at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] LumiT VST error > Message-ID: > ? ? ? ?<cagxwfc9ixxhjcdvdctakuchjzgcosxg_t7ncoozbf=ef_cubmq at="" mail.gmail.com=""> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello, i am having problems with VST with my Illumina data, > My values are all positive using lumiB "forcePositive" and my QC plots > looks fine, > Can anyone help me? > Thanks, > Paolo > > >> library("lumi") >> fileName<-"ANG.txt" >> x.lumi<-lumiR.batch(fileName) > Inputting the data ... > Annotation columns are not available in the data. > Duplicated IDs found and were merged! > > Adding nuID to the data ... > Please provide Illumina ID Mapping library! > Perform Quality Control assessment of the LumiBatch object ... > Warning message: > In as.vector(data) : si ? prodotto un NA per coercizione >> lumi.T<-lumiT(x.lumi) > Perform vst transformation ... > 2012-03-13 15:33:15 , processing array ?1 > Errore in if (any(std < 0)) { : > ?valore mancante dove ? richiesto TRUE/FALSE >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Italian_Italy.1252 ?LC_CTYPE=Italian_Italy.1252 > LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C > [5] LC_TIME=Italian_Italy.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] limma_3.6.9 ? ?lumi_2.2.1 ? ? Biobase_2.10.0 > > loaded via a namespace (and not attached): > ?[1] affy_1.28.1 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.1 > AnnotationDbi_1.12.1 ?DBI_0.2-5 ? ? ? ? ? ? grid_2.12.1 > ?[7] hdrcde_2.15 ? ? ? ? ? KernSmooth_2.23-4 ? ? lattice_0.19-13 > MASS_7.3-9 ? ? ? ? ? ?Matrix_0.999375-46 ? ?methylumi_1.6.1 > [13] mgcv_1.7-2 ? ? ? ? ? ?nlme_3.1-97 ? ? ? ? ? preprocessCore_1.12.0 > RSQLite_0.10.0 ? ? ? ?tools_2.12.1 ? ? ? ? ?xtable_1.6-0 > >