[BioC] simple limma question (read.ilmn)

[Kripa R]

No worries, it was a problem on my end. All sorted out now, thanks for the quick response! And yes ill definitely look into updating my R thanks :)

Kripa


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-----Original Message-----
From: Wei Shi <shi at wehi.EDU.AU>
Date: Thu, 8 Dec 2011 02:15:00 
To: <kripa777 at hotmail.com>
Cc: <bioconductor at r-project.org>
Subject: Re: [BioC] simple limma question (read.ilmn)

Dear Kripa,

Were you bead summary data from Illumina GenomeStudio/BeadStudio output, or from some other source? The read.ilmn function has been in place for two years and I haven't seen such a problem.

BTW, your R is quite old. You should update it to the latest version, although this won't solve your problem.

Cheers,
Wei

On Dec 8, 2011, at 8:49 AM, Kripa R wrote:

> 
> Hello everyone,
> When I try to load my illumina bead summary data into limma i get the following error msg:
> 
> library(limma)
> 
> x <- read.ilmn(files="ProbeProfile.txt",
> 
>                ctrlfiles="ControlProbeProfile.txt")
> 
> Error in dimnames(x) <- dn : 
>  length of 'dimnames' [1] not equal to array extent
> 
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=English_Canada.1252 
> [2] LC_CTYPE=English_Canada.1252   
> [3] LC_MONETARY=English_Canada.1252
> [4] LC_NUMERIC=C                   
> [5] LC_TIME=English_Canada.1252    
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets 
> [6] methods   base     
> 
> other attached packages:
> [1] limma_3.6.9
> 
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
> Any suggestions would be greatly appreciated! 
> Thanks,
> 
> 
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