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Hi Yogi, First, update your Bioc packages... I believe the current version of lumi is 1.4.0... Also, try looking at the objects you create before going to the next step. Is the 'raw' object looking like what you expect? simply type 'raw', or 'boxplot(raw)'. Cheers, Cei Yogi Sundaravadanam wrote: > Hi all > > > > I tried doing VST and the following error occurred and I?m stuck. I?d > really appreciate any thoughts or suggestions on this please. > > > > >> library(lumi) >> > > >> raw <- lumiR("Sample_Gene_Profile.txt") >> > > Warning messages: > > 1: closing unused connection 4 (Sample_Gene_Profile.txt) > > 2: closing unused connection 3 (Sample_Gene_Profile.txt) > > >> lumi.T <- lumiT(raw) >> > > 2008-02-07 09:29:07 , processing array 1 > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : > > > 0 (non-NA) cases > > > > > > >> sessionInfo() >> > > R version 2.6.0 (2007-10-03) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MON > ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia. 1252 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > > > [8] base > > > > other attached packages: > > [1] limma_2.12.0 lumi_1.2.0 annotate_1.16.1 > > [4] xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 > > [7] DBI_0.2-4 mgcv_1.3-27 affy_1.16.0 > > [10] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 > > > > Thanks heaps > > Yogi > > > > > > _____ > > Please Note: The message is intended only for the addressee. If you > receive this message in error please do not publish, distribute, or copy > it. Please advise the AGRF by telephone or email, and delete this > message from your computer. > > > > > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Cei Abreu-Goodger, PhD Wellcome Trust Sanger Institute Computational and Functional Genomics Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.