[BioC] GCRMA with HG-U95A and HG-U95Av2

Nicolas STRANSKY Nicolas.Stransky at curie.fr
Tue Dec 5 19:01:10 CET 2006


I'm trying to normalize HG-U95A and HG-U95Av2 chips with GCRMA.
I have tried two methods that were described on this list but have been
unsuccessful with both.

The first one was proposed by Zhijin Wu and adapted by Vincent Detours
It involved combineAffyBatch. I could not get it to work, it always ends
up with the following error:

> affinity.info1=compute.affinities("hgu95a")
Computing affinities.Done.
> affinity.info2=compute.affinities("hgu95av2")
Computing affinities.Done.
> affinity.mix12=combineAffyBatch(list(affinity.info1,affinity.info2),
c("hgu95aprobe","hgu95av2probe"), "hgu95av12new")
package:hgu95aprobe     hgu95aprobe
package:hgu95av2probe   hgu95av2probe
197193 unique probes in common
Error in "dimnames<-.data.frame"(`*tmp*`, value = list(c("Batch 1: ",  :
        invalid 'dimnames' given for data frame

The second solution involves the packages created by Ben Bolstad
(http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html) and the sample R
code from http://bmbolstad.com/misc/mixtureCDF/mixtureCDFexample.R.

> My.version1<- ReadAffy(celfile.path="./A")
> My.version2<- ReadAffy(celfile.path="./Av2")
> my.merged <-
> gcrma(my.merged)
Attaching package: 'hgu95av12mixcdf'
Adjusting for optical effect..............................Done.
Computing affinities[1] "Checking to see if your internet connection
Error in getProbePackage(probepackagename) :
        You do not have write access to /usr/local/lib/R/site-library
Please check your permissions or provide a different 'lib' parameter.

In order to correct this error, I have tried to apply so solution
described here:
But the package I create is not installable for an unknown reason.

# R CMD INSTALL /tmp/hgu95av12mixprobe_1.14.0.tar.gz
* Installing *source* package 'hgu95av12mixprobe' ...
** R
** data
** help
 >>> Building/Updating help pages for package 'hgu95av12mixprobe'
     Formats: text html latex example
  hgu95av12mixprobe                 text    html    latex   example
** building package indices ...
Error in load(zfile, envir = envir) : ReadItem: unknown type 101
Execution halted
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/site-library/hgu95av12mixprobe'

So has anybody been successful for a GCMRA normalization with U95A and
U95Av2 chips ?

Thanks for any help,
Équipe Oncologie Moléculaire             http://www.curie.fr/equipe/301
Institut Curie - UMR 144 - CNRS                 Tel : +33 1 42 34 63 40
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