[BioC] combineAffyBatch for HG-U133A and HG-U133Av2 GeneChips

[Wolfgang Huber]

Hi Kellie,

I am sorry - I think as one of the authors of matchprobes I should be able
to answer your question but it seems I can't fully parse it.

I am not sure whether this is the answer, but you can remove unwanted
probe sets from the CDF environment that resulted from combineAffyBatch.

What exactly do you want to do you?
Is RMA failing, and where/what with?

Best wishes
 Wolfgang


<quote who="Kellie J. Archer, Ph.D.">
> I used the combineAffyBatch function in the matchprobes library to
> merge data from HG-U133A and HG-U133Av2 GeneChips, which seemed to
> work well. However, the difference between the two chips (with respect
> to the probes interrogated) seem to be very minor, most notable is
> that the control probe sets for ribosomal RNAs were on the HG-U133A
> chips but are not on the HG-U133Av2 chip. However, after applying the
> combineAffyBatch function, the resulting $dat includes 5 of these rRNA
> probes. Additionally, there are intensities reported for the version 2
> chips. However, for other probe sets I did compare a sample of their
> PM/MM intensities against those in GCOS probe tiling view and they
> appear to be accurate.  My question is, how can I create an AffyBatch
> object that omits these 5 pm/mms so I can apply rma() to the merged
> dataset? I am running R 1.9.1.
>
> This is the code I used:
> ### Old chips ###
> library(affy)
> library(hgu133acdf)
> hgu133a<-ReadAffy(filenames=filenames1)
>
> ### New chips ###
> library(hgu133a2cdf)
> hgu133a.2<-ReadAffy(filenames=filenames2)
>
> ### Merge both sets
> library(matchprobes)
> both<-combineAffyBatch(list(hgu133a,hgu133a.2),c("hgu133aprobe","hgu13
> 3a2probe"),"newhgu133",verbose=TRUE)
> newhgu133<-both$cdf
>
> ###Check if rRNA probes omitted
> pn<-names(unlist(indexProbes(both$dat,"pm")))
> pn[grep("AFFX-r2-H",pn)]
> [1] "AFFX-r2-Hs18SrRNA-3_s_at1" "AFFX-r2-Hs18SrRNA-3_s_at2"
> [3] "AFFX-r2-Hs18SrRNA-5_at"    "AFFX-r2-Hs18SrRNA-M_x_at1"
> [5] "AFFX-r2-Hs18SrRNA-M_x_at2"
>
> Best,
> Kellie J. Archer, Ph.D.
> Assistant Professor, Department of Biostatistics
> Virginia Commonwealth University
> 1101 East Marshall St. B1-066
> Richmond, VA 23298-0032
> phone: (804) 827-2039
> fax: (804) 828-8900
> e-mail: kjarcher at vcu.edu
> website: www.people.vcu.edu/~kjarcher
>
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>


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber