Hi list, I have some questions about using new version of Limma and/or R. I have read that the last version of Limma have changes about reading GAL files. I am working with several input files coming from ScanArray scanner and I need to read necessarily a GAL file, I don?t have problems with the R version showing below and Limma 1.8 platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 0.1 year 2004 month 11 day 15 language R But When I run the same script(see below) under Limma v. 1.9.3 and R 2.1.0 I got this error >files <- dir(pattern="\\.txt"); # >RG <- read.maimages(files, columns=list(Rf="Ch1 Median",Gf="Ch2 Median",Rb="Ch1 B Median",Gb="Ch2 B Median")); # > RG$genes <- readGAL(); Error in list.files(path, pattern, all.files, full.names, recursive) : invalid 'pattern' regular expresion I need to use the last version of Limma because I also want to use the "normexp" background correction. I would like to know how I can solve this problem; any help will be much appreciated. I send you as attachment a small GAL file with just few rows as an example. Thank you for your help. Manuel ______________________________________________ Nuevos servicios, m?s seguridad -------------- next part -------------- ATF 1 1 5 Type=GenePix ArrayList V1.0 Block Row Column ID Name 1 1 1 gi|18150858:20626-20940 putative transcriptional repressor 1 1 2 gi|18150858:20626-20940 putative transcriptional repressor 1 1 3 gi|18150858:c106375-105110 putative mating pair formation protein 1 1 4 gi|18150858:c106375-105110 putative mating pair formation protein 1 1 5 DMSO Control_0 1 1 6 DMSO Control_0 1 1 7 DMSO Control_0 1 1 8 DMSO Control_0 1 1 9 gi|18150858:22773-23357 putative transcriptional regulator protein 1 1 10 gi|18150858:22773-23357 putative transcriptional regulator protein 1 1 11 gi|18150858:c109096-108704 hypothetical protein 1 1 12 gi|18150858:c109096-108704 hypothetical protein 1 1 13 DMSO Control_0 1 1 14 DMSO Control_0 1 1 15 DMSO Control_0 1 1 16 DMSO Control_0 1 2 1 gi|18150858:16158-16379 hypothetical protein 1 2 2 gi|18150858:16158-16379 hypothetical protein 1 2 3 gi|18150858:96571-96954 putative TraA protein 1 2 4 gi|18150858:96571-96954 putative TraA protein 1 2 5 DMSO Control_0 1 2 6 DMSO Control_0 1 2 7 DMSO Control_0 1 2 8 DMSO Control_0

This problem is caused by a new "feature" of R 2.1.0, stricter regular expression syntax. It has been fixed in limma 1.9.5. Gordon > Date: Thu, 19 May 2005 11:44:23 +0200 (CEST) > From: M Perez <perezperezmm@yahoo.es> > Subject: [BioC] Gal file and Limma > To: bioconductor@stat.math.ethz.ch > > Hi list, > > I have some questions about using new version of Limma > and/or R. > > I have read that the last version of Limma have > changes about reading GAL files. I am working with > several input files coming from ScanArray scanner and > I need to read necessarily a GAL file, I don?t have > problems with the R version showing below and Limma > 1.8 > > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 0.1 > year 2004 > month 11 > day 15 > language R > > > But When I run the same script(see below) under Limma > v. 1.9.3 and R 2.1.0 > > I got this error >>files <- dir(pattern="\\.txt"); > # >>RG <- read.maimages(files, columns=list(Rf="Ch1 > Median",Gf="Ch2 Median",Rb="Ch1 B Median",Gb="Ch2 B > Median")); > # >> RG$genes <- readGAL(); > Error in list.files(path, pattern, all.files, > full.names, recursive) : > invalid 'pattern' regular expresion > > > I need to use the last version of Limma because I also > want to use the "normexp" background correction. > > I would like to know how I can solve this problem; any > help will be much appreciated. > > I send you as attachment a small GAL file with just > few rows as an example. > > Thank you for your help. > Manuel > > > > > ______________________________________________ > > Nuevos servicios, m?s seguridad > -------------- next part -------------- > ATF 1 > 1 5 > Type=GenePix ArrayList V1.0 > Block Row Column ID Name > 1 1 1 gi|18150858:20626-20940 putative transcriptional repressor > 1 1 2 gi|18150858:20626-20940 putative transcriptional repressor > 1 1 3 gi|18150858:c106375-105110 putative mating pair formation protein > 1 1 4 gi|18150858:c106375-105110 putative mating pair formation protein > 1 1 5 DMSO Control_0 > 1 1 6 DMSO Control_0 > 1 1 7 DMSO Control_0 > 1 1 8 DMSO Control_0 > 1 1 9 gi|18150858:22773-23357 putative transcriptional regulator protein > 1 1 10 gi|18150858:22773-23357 putative transcriptional regulator protein > 1 1 11 gi|18150858:c109096-108704 hypothetical protein > 1 1 12 gi|18150858:c109096-108704 hypothetical protein > 1 1 13 DMSO Control_0 > 1 1 14 DMSO Control_0 > 1 1 15 DMSO Control_0 > 1 1 16 DMSO Control_0 > 1 2 1 gi|18150858:16158-16379 hypothetical protein > 1 2 2 gi|18150858:16158-16379 hypothetical protein > 1 2 3 gi|18150858:96571-96954 putative TraA protein > 1 2 4 gi|18150858:96571-96954 putative TraA protein > 1 2 5 DMSO Control_0 > 1 2 6 DMSO Control_0 > 1 2 7 DMSO Control_0 > 1 2 8 DMSO Control_0