[BioC] questions about U133A cdf packages

[James W. MacDonald]

Wenlei Liu wrote:

>I'm trying to use the U133A spike-in data set (Latin square data) to do some analyses. However, I can not load the cel files into R. I installed HG-U133A_tag_CDF.zip in R using "install package from local zip file" option, but still got the following error message. Does anyone know what's wrong?
>
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>>install.packages("E:/data/Liu/microarray/U133/HG-U133A_tag_CDF.zip", .libPaths()[1], CRAN = NULL)
>>    
>>
This looks like you are trying to install the cdf file you got from 
Affymetrix (which is incorrect). You need to do this:
library(reposTools)
install.packages2("hgu133atagcdf")

HTH,

Jim


>updating HTML package descriptions
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>>testData<-ReadAffy(widget=TRUE)
>>    
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>Loading required package: tkWidgets 
>Loading required package: tcltk 
>Warning messages: 
>1: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 
>2: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 
>3: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compress = compress) 
>  
>
>
>Your comments will be highly appreciated.
>
>Wenlei
>
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Facility
University of Michigan
Comprehensive Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109