[BioC] Combining A and B chips

[Wolfgang Huber]

Dear Adrien,

> I'm trying to integrate the results of two experiments, one involving
> moe430 A and B chips, the other moe430_2 chips.
> Hence I thought about combining AffyBatches from moe430 A and B into
> one, to get moe430_2 "equivalents".
>  
> This is relatively easy to do after processing (i.e. at the probeset
> level), but the trick is that I would really like to do this at the
> probe level (because I would like to normalize the combined chips
> together with moe430_2 chips - not sure if this make sense by the way).

It might indeed not make sense, if you use standard normalization 
methods, since in general you need a separate normalization 
transformation for each array.

What I would try is to set up big linear model with appropriate array 
effects (e.g. one background and one scale parameter for each array), 
and come up with an efficient enough method for fitting it. I don't know 
of any existing software for this - perhaps others do?

For the actual stitching the data together, you might want to check the 
code in the combineAffyBatch function in the matchprobes package; while 
it does not exactly do what you want, maybe some of it is reusable.

> 1) Does anyone know if there is a function written somewhere that could
> help?
>  
> 2) Or, would it be possible to create a moe430_2 AffyBatch object from
> scratch?
> (I could probably read an existing chip and replace the PMs and MMs but
> that's not very elegant, is it?)
>  
> 3) Or, if nothing else, would there be a function to do quantile
> normalization at the probeset level?
>  
> Thanks for any ideas...
> Adrien

Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber