[BioC] New Affy SpikeIn Data Set & Affy

Crispin Miller CMiller at PICR.man.ac.uk
Wed Aug 27 16:55:45 MEST 2003


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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
 
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