[BioC] HGU95a and HGU95av2 with gcrma

[Vincent Detours]

Dear all,

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/