[BioC] New Affy SpikeIn Data Set & Affy

[Rafael A. Irizarry]

the cdf env is already there. 

http://www.bioconductor.org/data/metaData.html

what is still missing is the probe 
sequence info package. we are working on that...


On Wed, 27 Aug 2003, James MacDonald wrote:

> You will have to use the makecdfenv package to make a cdf environment
> that affy can use. See the help for makecdfenv.
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> "laurent  buffat" <laurent.buffat at it-omics.com> 08/27/03 10:32AM
> >>>
> 
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>