[BioC] match probes: probesets with too few matches

[Wolfgang Huber]

Hi Margaret,

if you know in the first place that so many probesets are identical, and 
which ones, you could try to put the AffyBatches together yourself based 
on that information, using the MOE430Av2 CDF.

The main intention of the combineAffyBatch function is for situations 
where the correspondence between the chips is more complicated, that's 
why its output is as it is.

You could use "rm(..., envir=comb)" to delete the probesets that you 
don't like from the result of combineAffyBatch.

Hope this helps, best wishes
   Wolfgang

  Gardiner-Garden wrote:
> Hi, I have been using the function combineAffyBatch (match probes library)
> to combine the data for two mouse chips MOE430v2 (45101 probesets) and its
> subset chip MOE430Av2 (22690 probesets).
> According to Affymetrix the 22690 probesets in MOE430Av2 are identical in
> MOE430v2.
> 
> I ran the following:
> res <- combineAffyBatch(list(Data.430v2, Data.430Av2),c("mouse4302probe",
> "mouse430a2probe"), newcdf="comb")
> comb <- res$cdf
> 
> 
> This gave a combination expression set with 22702 probesets (ie 12 more
> probeset names than the subset chip MOE430Av2).
> 
> I looked to see the number of oligos matching in the different probesets
> prs <- mget(ls(comb), comb,  ifnotfound=NA)
> nrprobes <- sapply(prs, function(x) nrow(x))
> table(nrprobes)
> 
> 
> 
>>table(nrprobes)
> 
> nrprobes
>     1     2     3     4     5     8     9    10    11    20    21
>     7     2     1     1     1     1     4    11 22631    40     3
> 
> 
> 
> The probeset names that were not present on MOE430v2 all had less than 8
> oligos matching between the chip types.
> 
> I was wondering if anyone knew the best way to exclude such probesets in the
> expression set, or how to avoid this problem in the first place.
> 
> 
> Thanks and Regards
> Dr Margaret Gardiner-Garden
> 
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-- 
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