[BioC] Combining A and B chips

[Adaikalavan Ramasamy]

Agreed. Also see the following thread
   http://files.protsuggest.org/biocond/html/3268.html

Regards, Adai



On Fri, 2005-07-22 at 11:34 +0100, Wolfgang Huber wrote:
> 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
> 
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