[BioC] Fwd: problem with reading gpr files

Maciej Jończyk mjonczyk at biol.uw.edu.pl
Thu Mar 7 12:21:32 CET 2013

> From: konika chawla <chawla at 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 

Hope that helps

Best Wishes

Dr Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1

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