[BioC] affy: adding new probe set definitions and making rma expression summaries

[Mette Langaas]

1) Problem: want to add five probe sets (from existing probes) in
hgfocus-array and make expression summaries for all probesets (existing
+ five new) using rma (medianpolish)

2) Have: AffyBatch object, dsnorm, of normalized probes.

ds <- ReadAffy(filenames=paste(celcatalog,celfilenames,sep=""))
dsbgcorr <- bg.correct(ds,method="rma")
dsnorm <- normalize(dsbgcorr,method="quantiles")

3) Have: definition of the new probesets:
hlag <- "211528_x_at"
locpm <- unlist(pmindex(ds,hlag))
locmm <- unlist(mmindex(ds,hlag))

# the five new (overlapping...) probsets by redefining the original
probesets

hlaglocation <- list(HLAG1to7=cbind(pm=locpm[1:7],mm=locmm[1:7]),
                   HLAG8=cbind(pm=locpm[8],mm=locmm[8]),
                   HLAG9=cbind(pm=locpm[9],mm=locmm[9]),
                   HLAG10to11=cbind(pm=locpm[10:11],mm=locmm[10:11]),
                   HLAG9to11=cbind(pm=locpm[9:11],mm=locmm[9:11]))

4) Howto: how is it possible to "computeExprSet" (or related) with
method "medianpolish" for the new probesets located as given in
hlaglocation together with all the existing probesets in the AffyBatch
object dsnorm?

I have read through Bioconductor documentation and mail-list-questions
about affy, altcdfenvs, and sadly I am not able to understand 
how to do this :-(

I'm running 
> version
         _
platform i686-redhat-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    2
minor    1.1
year     2005
month    06
day      20
language R

Your help is greatly appreciated!

Best regards
Mette



-- 
Mette Langaas 
Department of Mathematical Sciences
Norwegian University of Science and Technology
NO-7491 Trondheim, Norway
Voice: +47-7359-1697    URL  : http://www.math.ntnu.no/~mettela
Fax  : +47-7359-3524    Email: mette.langaas at math.ntnu.no

-- 
Mette Langaas 
Department of Mathematical Sciences
Norwegian University of Science and Technology
NO-7491 Trondheim, Norway
Voice: +47-7359-1697    URL  : http://www.math.ntnu.no/~mettela
Fax  : +47-7359-3524    Email: mette.langaas at math.ntnu.no