[BioC] Combining HGU133A & HGU133B data

w.huber at dkfz-heidelberg.de w.huber at dkfz-heidelberg.de
Mon Sep 15 15:19:01 MEST 2003


On Mon, 15 Sep 2003, Laurent Gautier wrote:
> Wolgang Huber and Robert Gentleman have certainly a word to say about
> that. Did you check the function 'combine' in the package 'matchprobes'
> (section 'devel') ?

The combine function in the matchprobes package is useful for combining
data from different chip types. The combination is done on the
probe-level, before normalization, and it requires that there is an
appreciable overlap in probe sequences (as, for example, with
hu6800/hgu95av2 or mgu74a/mgu74av2). The combination is based on the
INTERSECTION of probes that have the same sequence, and from the point of
view of the expression matrix, it corresponds, loosely speaking, to a

What Adaikalavan is looking for is much simpler: something that works on
the UNION of all probes/genes on HGU133A and HGU133B, and from the point
of view of the expression matrix corresponds to an RBIND.

I am not aware of a simpler method for doing this than calling
new("exprSet", ....) with the arguments patched together from the
individual two HGU133A and HGU133B exprSets.

Best regards

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/mga/whuber

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