Question

limma read.maimages for scanarray express .csv files

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 9.7 years ago

sltucker at artsci.wustl.edu writes: > Hi, > > I am new to limma and am having problems reading Scanarray Express .csv > files into limma via read.maimages. I am running R version 2.4.1 and > limma version 2.9.17. > > I tried... > >>RG<-read.maimages(files, source="scanarrayexpress", path=path) > Error in readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file > In addition: Warning messages: > 1: input string 1 is invalid in this locale in: grep(pattern, x, I wonder if this is a locale issue. You may need to tell R to use a different encoding for text. It would be helpful if you provided the output of sessionInfo() after you have received these warning messages (it will include your current locale info). + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

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ADD COMMENT • link 17.1 years ago Seth Falcon ★ 7.4k

score 0 · Answer 1 · 2007-05-01

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 9.7 years ago

Hi, [I've put the bioconductor list back in cc, please keep the Q&A on-list so that others can benefit too] sltucker at artsci.wustl.edu writes: > Thanks for the help. My sessionInfo() is > > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 It might be worth setting your locale to "C" and seeing if the error is the same. Sys.setlocale(locale="C") + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

ADD COMMENT • link 17.1 years ago Seth Falcon ★ 7.4k

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I set my locale to "C", and now have a different error. > RG<-read.maimages(files, source="scanarrayexpress", path=path, columns=list(Rf="Ch1 Median", Rb="Ch1 B Median", Gf="Ch2 Median", Gb= "Ch2 B Median")) Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected My new sessionInfo() is > sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C/C/C/C/C/en_US.UTF-8 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: gtools limma "2.3.0" "2.9.17" Thanks! > Hi, > > [I've put the bioconductor list back in cc, please keep the Q&A > on-list so that others can benefit too] > > sltucker at artsci.wustl.edu writes: >> Thanks for the help. My sessionInfo() is >> >> R version 2.4.1 (2006-12-18) >> i386-apple-darwin8.8.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > It might be worth setting your locale to "C" and seeing if the error > is the same. > > Sys.setlocale(locale="C") > > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research > Center > http://bioconductor.org >

ADD REPLY • link 17.1 years ago sltucker@artsci.wustl.edu ▴ 20