[BioC] New Affy SpikeIn Data Set & Affy

James MacDonald jmacdon at med.umich.edu
Wed Aug 27 11:47:12 MEST 2003

You will have to use the makecdfenv package to make a cdf environment
that affy can use. See the help for makecdfenv.


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "laurent  buffat" <laurent.buffat at it-omics.com> 08/27/03 10:32AM

Dear all,

Affymetrix provied a new SpikeIn data Sets

But, this data sets requires a special, alternate chip description
because there is eight artificial clones

And when I try to load/bg correct and normalise the data in R, I have
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
for unknown  could not be found.
Try downloading the unknowncdf package from

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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