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

[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