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

[Wolfgang Huber]

Hi Kellie,

 > I would like to remove unwanted probeset from the resulting $dat
 > object prior to applying rma or any other expression summary method.

I think it should not make much of a difference whether you remove these 
probesets before or after RMA, since the R in RMA stands for "Robust".

 > How would I remove these from the affybatch object prior to rma?

You can remove probesets by some code like this

	comb <- both$cdf
	gn <- ls(comb)
	rm(grep("AFFX-r2-H", gn, value=TRUE), envir=comb)

I haven't tested this but I hope you get the idea.

 > One other question is that I have been trying to ascertain why these
 > probes were retained by combineAffyBatch in the first place. How can
 > one investigate that most efficiently?

You can copy the code for the function combineAffyBatch from the 
corresponding file in the "package source" tar.gz file, and then add 
various checkpoints and plots to see what is going on.

Hope this helps

Best wishes
  Wolfgang


------------------------------------
Kellie J. Archer, Ph.D. wrote:
> Thanks Wolfgang,
> 
> I would like to remove unwanted probeset from the resulting $dat
> object prior to applying rma or any other expression summary method.
> So far, I have been able to apply rma to the resulting $dat object
> then remove unwanted probe sets from it using
> 
> both.rma<-rma(both$dat)
> gn<-geneNames(both.rma)
> both.rma.2<-both.rma[-grep("AFFX-r2-H",gn)]
> 

> One other question is that I have been trying to ascertain why these
> probes were retained by combineAffyBatch in the first place. How can
> one investigate that most efficiently?
> 
> Thanks again,
> Kellie Archer
> -------------------
> 
>>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
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
>>
>>
>>-------------------------------------
>>Wolfgang Huber
>>European Bioinformatics Institute
>>European Molecular Biology Laboratory
>>Cambridge CB10 1SD
>>England
>>Phone: +44 1223 494642
>>Http:  www.dkfz.de/abt0840/whuber
>>-------------------------------------
>>
>>
> 
> 


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