[BioC] Combining HGU133A & HGU133B data

[w.huber at dkfz-heidelberg.de]

Hi

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
CBIND.

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

-------------------------------------
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