[BioC] Re: HGU95a and HGU95av2 with gcrma and combineAffybatch

[Vincent Detours]

Dear all,

Here is follow up on a recent posting regarding join gcrma
normalisation of hu95a and hgu95av2 chips, or any such pairs of
GeneChips, an issue that came up several times on the list.  Zhijin Wu
kindly worked out the following solution, which I applied sucessfully:

-----------------------------------------------
library(matchprobes)
library(hgu95acdf)
library(hgu95av2cdf)
library(hgu95aprobe)
library(hgu95av2probe)
library(gcrma)

affinity.info1=compute.affinities("hgu95a")
affinity.info1=new("AffyBatch",exprs=exprs(affinity.info1),cdfName=cdfName(affinity.info1),nrow=640,ncol=640)
affinity.info2=compute.affinities("hgu95av2")
affinity.info2=new("AffyBatch",exprs=exprs(affinity.info2),cdfName=cdfName(affinity.info2),nrow=640,ncol=640)
affinity.mix12=combineAffyBatch(list(affinity.info1,affinity.info2),
  c("hgu95aprobe","hgu95av2probe"), "hgu95av12new")
hgu95av12newcdf=affinity.mix12$cdf

N1=dim(exprs(affinity.info1))[1]
rawc1 <- ReadAffy(celfile.path="~/data95av2")

N2=dim(exprs(affinity.info2))[1]
rawc2 <- ReadAffy(celfile.path="~/data95a")

com12 <- combineAffyBatch(list(rawc1, rawc2), c("hgu95aprobe",
"hgu95av2probe"), "hgu95av12new")
hgu95av12new=com12$cdf

save(hgu95av12new, file="hgu95av12newcdf.Rda", compress=T)
hgu95av12new=hgu95av12newcdf=com12$cdf

affinity.info=affinity.mix12$dat
exprs(affinity.info)=matrix(exprs(affinity.info)[,1],ncol=1)

rm(rawc1, rawc2, affinity.info1, affinity.info2, affinity.mix12)

es=gcrma(com12$dat,affinity.info=affinity.info)
-----------------------------------------------

I hope this help.

Vincent Detours


On Mon, 22 Nov 2004, Vincent Detours wrote:

> I need to run gcrma on HGU95a and HGU95av2 arrays. Although the
> issue came up on the list, no answer was posted.
>
> I downloaded hgu95av12mixcdf from
> http://www.stat.berkeley.edu/~bolstad/mixtureCDF/MixtureCDF.html
> as recommended in previous postings.  RMA ran fine with this later
> package.
>
> In order to run gcrma, I created a hgu95av12mixprobe package with
> ---------
> makeProbePackage("hgu95av12mix",
>                  datafile   = "HG-U95Av2_probe_tab",
>                  outdir     = ".",
>                  maintainer = "Vincent Detours, <vdetours at ulb.ac.be>",
>                  version    = "0.0.1",
>                  force      = TRUE)
> ---------
>
> It worked fine. I then installed and loaded all the above data
> package with "library" and made a combined affybatch with
> ---------
> rawc <- combineAffyBatch(list(rawc1, rawc2), c("hgu95av2probe",
> "hgu95aprobe"), "hgu95av12mix")
> ---------
> which ran with no complains.
>
> and then ran gcrma:
> -----------------------
> > es <- gcrma(rawc$dat)
> Computing affinities.Error in compute.affinities(cdfName(object),
> verbose = verbose) :
> 	NAs are not allowed in subscripted assignments
> >
> -----------------------
>
> Any idea about what went wrong?
>
> An idea would be to make a package from the cdf environment produced
> by combineAffyBatch. But I don't see how to do this from
> make.cdf.package, which takes only Affymetrix CDF files as argument.
> How to make gcrma to use rawc$cdf?
>
> Thanks for your help and for all the great work!
>
> Vincent Detours, Ph.D.
> IRIBHM
> Bldg C, room C.4.116
> ULB, Campus Erasme, CP602
> 808 route de Lennik
> B-1070 Brussels
> Belgium
>
> Phone: +32-2-555 4220
> Fax: +32-2-555 4655
>
> E-mail: vdetours at ulb.ac.be
>
> URL: http://homepages.ulb.ac.be/~vdetours/
>