[BioC] problems with gcrma just.gcrma

[James W. MacDonald]

Hi Elisabetta,

Elisabetta Manduchi wrote:
> Hello,
> I'm trying to use just.gcrma with data from Affy MGU74Av2 and am getting 
> the error at the bottom of what's copied below re read.probematrix. I'm 
> running version 2.4.0 of R and gcrma version 2.6.0. The mgu74av2 packages 
> being downloaded are version 1.14.0.
> Can anybody advice on what I can do to overcome this?

That error usually means that you are not pointing to celfiles with your 
filenames argument. What do you get if you type

cel.files

at the R prompt? It is often easier to use filenames=list.celfiles().

Best,

Jim


> Thanks,
> Elisabetta
> ---
> 
>>data.gcrma<-just.gcrma(filenames=cel.files, type=c("fullmodel"), normalize=T, optimize.by=c("memory"), fast=T, samepleNames=sample.names)
> 
> 
> Computing affinities[1] "Checking to see if your internet connection 
> works..."
> trying URL 
> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2cdf_1.14.0.zip'
> Content type 'application/zip' length 1340750 bytes
> opened URL
> downloaded 1309Kb
> 
> package 'mgu74av2cdf' successfully unpacked and MD5 sums checked
> 
> The downloaded packages are in
>          C:\Documents and Settings\Elisabetta Manduchi\Local 
> Settings\Temp\Rtmpc7v1qb\downloaded_packages
> updating HTML package descriptions
> [1] "Checking to see if your internet connection works..."
> trying URL 
> 'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2probe_1.14.0.zip'
> Content type 'application/zip' length 2396326 bytes
> opened URL
> downloaded 2340Kb
> 
> package 'mgu74av2probe' successfully unpacked and MD5 sums checked
> 
> The downloaded packages are in
>          C:\Documents and Settings\Elisabetta Manduchi\Local 
> Settings\Temp\Rtmpc7v1qb\downloaded_packages
> updating HTML package descriptions
> .Done.
> Error in read.probematrix(filenames = filenames, which = "pm", cdfname = 
> cdfname) :
>          VECTOR_ELT() can only be applied to a 'list', not a 'symbol'
> ---
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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