[BioC] combining hgu133a hgu133b

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Thu Nov 11 20:23:06 CET 2004

I asked this question before and used almost the same subject line as
you did (mine was "Combining HGU133A & HGU133B data"). See

IMHO, it is better to do 1). 

But if you insist on 2), this may be possible using the suggestion in
Laurent Gautier's reply but I think there might new functions since the
posting that could do this.

As Crispin Miller suggested, you have 2000+ probesets that you can to
use as quality check or calibrate.

On Thu, 2004-11-11 at 17:09, Auer Michael wrote:
> I would like to know what the best solution is in analyzing data from the
> same yource hybridized to hgu133a and hgu133b chips.
> 1. Shall the arrays be normalized sperately and merged afterwards?
>   But then the question arises how to annotate, because there is no such
> environment available
> 2. Shall the arrays be merged into one affyBatch before normalization? How
> can I do smth like this. Which packages have the appropriate functions?
> 3. What about the similar sequences? Is there smth to worry about?
> 4. Is this not a problem often encounterd by analysits? Is there such a
> function which merges the two environments automatically?
> Thanks a lot for your help
> Michael
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Adaikalavan Ramasamy                    ramasamy at cancer.org.uk
Centre for Statistics in Medicine       http://www.ihs.ox.ac.uk/csm/
Cancer Research UK                      Tel : 01865 226 677
Old Road Campus, Headington, Oxford     Fax : 01865 226 962

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