[BioC] limma read.maimages for scanarray express .csv files

[Gordon K Smyth]

Dear Sarah,

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
read.maimages call.

If your problem persists, you need to give send the leading lines of your data file, up to the
start of the data.

Best wishes
Gordon

> 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
> 	files
> 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
>
>> 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