[BioC] New Affy SpikeIn Data Set & Affy

[Crispin Miller]

Hi,
It looks like you need to download the hgu133atagcdf data set from www.bioconductor.org
After you've run ReadAffy, you probably need to set the cdf name to "hgu133atag"

i.e.

eset <- ReadAffy(...);
eset at cdfName <- "hgu133atag"
eset.rma     <- rma(eset)

... or whatever.


Hope that helps!
Crispin

> -----Original Message-----
> From: laurent buffat [mailto:laurent.buffat at it-omics.com]
> Sent: 27 August 2003 15:33
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] New Affy SpikeIn Data Set & Affy
> 
> 
> 
> Dear all,
> 
> Affymetrix provied a new SpikeIn data Sets
> https://www.affymetrix.com/support/datasets.affx
> 
> But, this data sets requires a special, alternate chip 
> description file
> (CDF),
> because there is eight artificial clones
> 
> And when I try to load/bg correct and normalise the data in 
> R, I have an
> error at the bg.correct step :
> 
> > exp <- ReadAffy(filenames=list.cel,phenoData=phenodata,verbose=T)
> Ok, no problem
> 
> > exp <- bg.correct(exp, method = "rma",verbose=T)
> 
> Sample :  1Error in .local(object, ...) : Information about 
> probe locations
> for unknown  could not be found.
> Try downloading the unknowncdf package from
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> 
> 
> The correct CDF is available at affymetrix.
> I have try to put this CDF in the data directory (as it was 
> necessary in the
> first version of affy), but it doesn' work.
> 
> How I can read this data with affy ?
> 
> Thanks for your help.
> 
> L. Buffat
> 
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> Bioconductor at stat.math.ethz.ch
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>
 
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