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On Mar 18, 2008, at 7:49 PM, Chintanu wrote: > Hi! > > I'd like to ask 3-basic questions on Bioconductor: > > * Having the target file, gpr and gal file all in the same directory > as R, > what the following error message is actually referring to : > >> library(arrayQuality) >> TargetInfo <- read.marrayInfo ("targets11.txt") >> mraw <- read.GenePix (targets = TargetInfo) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > In file(con, "r") : > cannot open file './B1a', reason 'No such file or directory' Given your example below my guess is that in the targets file you call your files say B1a where it should be B1a.gpr We probably need to see the contents of the target file if this doesn't help. Kasper > > >> sessionInfo() > > R version 2.6.0 (2007-10-03) > > i386-pc-mingw32 > > locale: > > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > > > attached base packages: > > [1] grid tools stats graphics grDevices datasets tcltk > utils methods base > > > > other attached packages: > > [1] arrayQuality_1.14.0 RColorBrewer_1.0-2 gridBase_0.4-3 > hexbin_1.12.0 lattice_0.17-6 convert_1.14.0 > Biobase_1.16.3 > > [8] marray_1.16.0 limma_2.12.0 svSocket_0.9-5 > svIO_0.9-5 R2HTML_1.58 svMisc_0.9-5 > svIDE_0.9-5 > > > > * Again, I'm also getting an Error message with the Gal file > [sessionInfo() > is same as above]. > >> library(arrayQuality) > >> targets <- readTargets("targets11.txt") > >> RG <- read.maimages(targets$FileName,source="genepix",ext="gpr") > Read B1a.gpr > Read B1b.gpr > Read B1cDS.gpr >> names(RG$genes) > [1] "Block" "Row" "Column" "ID" "Name" > >> RG$genes <- readGAL() > Error in readGAL() : Cannot find ID and Name columns in GAL file > > > > * I have gone through the short description given in LIMMA User's > guide, 18 > April 2007 (from page 32 onwards) on microarry design matrix. Is > there any > other reference(s) one can refer to ? > > Thanks for any comment and help, > > Chintanu > > [[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