[BioC] problems with affy package

w.huber at dkfz-heidelberg.de w.huber at dkfz-heidelberg.de
Tue Oct 28 10:41:52 MET 2003

Hi Stephen,

are you trying to read in the CEL files from different (sub)chips into one
AffyBatch? The design of the affy package is such that these belong into
different AffyBatches, and only after normalization/expression measure
calculation you are supposed to merge ('rbind') them together.

Best wishes

Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber

On Tue, 28 Oct 2003, Stephen Moore wrote:

> Dear All,
> I have been trying to generate expression measures from the mu6500 chip.
> I have downloaded the four subchip cdf files, however when I import the
> cel file data as a whole, it stalls on certain chips, for example, it
> stalled on the subB cel file and said it was not of subA type.  When I
> carry out these chips individually they work.  Is there a certain
> sequence in which the process has to be carried out or am I missing
> something quite trivial.  Many thanks for any help you can give me.
> Cheers

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