[BioC] New Affy SpikeIn Data Set & Affy

[James MacDonald]

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