
Dear all,

I'd like to combine hgu133a and hgu133a2 chips in a single data analysis 
(gcrma, ...).
I used combine.AffyBatch to get both the combined affybatch and the hybrid 
CDF, and all worked smoothly.
However, I get into trouble when running rma, it looks like the new CDF 
environment is not known to R; that is further confirmed in using 
getCdfEnvAffy, as can be seen below.
Indeed, I'd like to background correct the raw data with gcrma, but that 
can be done separately on both data sets (is it correct ?), which will 
then be combined after for normalisation and summarization with rma. 
However, the problem remains.
Has anybody been successful at combining hgu133a and hgu133a2 ?

I'm running R 2.3.1 and BioC 1.8 , on Win XP.
rawdata.p6p12 and rawdata.p15 are plain affybatches;

> library(matchprobes)
> 
combined=combineAffyBatch(list(rawdata.p6p12,rawdata.p15),c("hgu133aprobe","hgu133a2probe"),newcdf="hgu133aa2")
package:hgu133aprobe    hgu133aprobe 
package:hgu133a2probe   hgu133a2probe 
241837 unique probes in common
>
> rawdata.p6p15=combined$dat
> hgu133aa2cdf=combined$cdf
>
> str(rawdata.p6p15)
Formal class 'AffyBatch' [package "affy"] with 10 slots
  ..@ cdfName     : chr "hgu133aa2"
  ..@ nrow        : num 0
  ..@ ncol        : num 0
  ..@ exprs       : num [1:483674, 1:21]  662 1078 1631 4645 6793 ...
  lot of stuff deleted
 
> eset=rma(rawdata.p6p15)
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain hgu133aa2
Library - package hgu133aa2cdf not installed
Data for package affy did not contain hgu133aa2cdf
Bioconductor - hgu133aa2cdf not available
> library(altcdfenvs)
Loading required package: makecdfenv
> getCdfEnvAffy(rawdata.p6p15)
Error in getCdfInfo(abatch) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain hgu133aa2
Library - package hgu133aa2cdf not installed
Data for package affy did not contain hgu133aa2cdf
Bioconductor - hgu133aa2cdf not available


Thanks for your help.
Jean-Louis

====================================================
Jean-Louis Ruelle
GlaxoSmithKline Biologicals, R&D
Rue de l'Institut, 89
1330 Rixensart
Belgium

Phone : + 32-2-6568451
Fax :   +32-2-6568436
email :  jean-louis.ruelle@gskbio.com



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