[BioC] gcrma problem

James W. MacDonald jmacdon at med.umich.edu
Tue Aug 12 18:47:16 CEST 2008

Hi Glyn,

You want makeProbePackage() in the matchprobes package (plus the 
probe_tab file for your chip, which hopefully you got from Affy).



Glyn Bradley wrote:
> Hi all,
> I'm using a custom affy chip, I have made the cdf using makecdfenv, 
> installed it using R CMD INSTALL ..., and I can use the package affy 
> sucessfully to do rma normalisations etc, but when trying to carry out 
> gcrma in with the package gcrma, I get  :
> eset <- gcrma(Data)
> Adjusting for optical effect...Done.
> Computing affinities[1] "Checking to see if your internet connection 
> works..."
> [1] "Environment XXXXXaprobe was not found in the Bioconductor repository."
> Error in get(probepackagename) : variable "XXXXXaprobe" was not found
> How can I make/ install a custom XXXXaprobe file
> anyone? Thanks in advance
> Glyn
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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