[BioC] annotation hgu133plus2 problem,

[James W. MacDonald]

Saurin D. Jani wrote:
> Hi BioC,
> 
> When I am trying to get annotations of ALL GENEs on my hgu133plus2 GeneChip.
> Please see below output...here my R script is hanging on computer. I am using
> Linux 64 bit with 2 GB RAM memory with 45 CEL files.
> 
> 
>>AnnTable1 <- aafTableAnn(AllGenes,hgu133plus2,AnnCols[2]);
> 
> Loading required package: reposTools
> [1] "You have package hgu133plus2 but the incorrect version"
> Warning message:
> cannot open: HTTP status was '404 Not Found'
> Note:
> http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.3
> does not seem to have a valid repository, skipping
> Warning message:
> Failed to read replisting at
> http://www.bioconductor.org/packages/data/annotation/stable/bin/windows/contrib/2.3
> in: getReplisting(repURL, repFile, method = method)
> ################################################################

It's trying to get the correct version of hgu133plus2 and failing. You 
might try:

source("http://www.bioconductor.org/biocLite.R")
biocLite("hgu133plus2")

Another alternative is to go to the devel metaData page on BioC, 
download the correct tar.gz file and install using R CMD INSTALL.

HTH,

Jim

> Thank you in advance,
> Saurin
> 
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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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