Dear Dr Maciej
I used myfiles <- dir(pattern=3D"gpr") also reads the gpr files, but just for trying it again I created a target file as prescribe on limma documentation.
and then try to read the gpr files, it still gives the same error.
here is the piece of code I used 
library(limma)
targets <- readTargets("targets.txt")
f <- function(x) as.numeric(x$Flags > -99)
RG <- read.maimages(targets, source="genepix", wt.fun=f)
and the error is : 
"Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected"
I guess it is something to do with the gpr files, but don't know what.
Any other ideas?
Thanks
Konika





On Mar 7, 2013, at 12:21 PM, Maciej Jończyk wrote:

>> From: konika chawla <chawla@bio.ntnu.no>
>> 
>> Subject: [BioC] Fwd: problem with reading gpr files
>> (Posting it a second time ..) Hi I am new to analyzing gpr files and I am getting an error in the first stage of reading them.
>> 
>> 
>>       library(limma) myfiles <- dir(pattern=3D"gpr") RG <- read.maimages(myfiles, source=3D"genepix")
>> 
>>  Where also I get the error=20
>> 
>>       Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected
>> 
>> I tried to look for solution but couldn't find any except that the 'gpr files should be used as obtained from genepix'.
> 
> You're not so far from correct commands.
> Please look at limma documentation - there are some clear explanations.
> You have to make targets file and read it with readTargets,
> then you should use read.maimages using target frame and directory with gprs.
> 
> Hope that helps
> 
> Best Wishes
> 
> -- 
> Dr Maciej Jonczyk,
> Department of Plant Molecular Ecophysiology
> Faculty of Biology, University of Warsaw
> 02-096 Warsaw, Miecznikowa 1
> Poland
> 
> 
> 
> -- 
> This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com

Konika Chawla
PhD Student
Department of Biology
NTNU 





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