[BioC] limma read.maimages for scanarray express .csv files
Gordon K Smyth
smyth at wehi.EDU.AU
Thu May 3 15:13:54 CEST 2007
A problem with your code is that you are trying to read a comma-separated file whereas limma
assumes that files are tab-delimited. To read a csv file, you need to specify sep="," in the
If your problem persists, you need to give send the leading lines of your data file, up to the
start of the data.
> Date: Tue, 1 May 2007 13:55:55 -0500 (CDT)
> From: sltucker at artsci.wustl.edu
> Subject: Re: [BioC] limma read.maimages for scanarray express .csv
> To: "Seth Falcon" <sfalcon at fhcrc.org>
> Cc: sltucker at artsci.wustl.edu, bioconductor at stat.math.ethz.ch
> 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
> R version 2.4.1 (2006-12-18)
> attached base packages:
>  "stats" "graphics" "grDevices" "utils" "datasets" "methods"
> other attached packages:
> gtools limma
> "2.3.0" "2.9.17"
>> [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)
>> It might be worth setting your locale to "C" and seeing if the error
>> is the same.
>> + seth
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
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