[BioC] new CDF env from combineAffyBatch is not recognized

[James W. MacDonald]

Hi Jean-Louis,

jean-louis.ruelle at gskbio.com wrote:
> 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

I think the problem here is that you have named your cdf hgu133aa2cdf, 
but the cdfname of your AffyBatch is hgu133aa2. Try

cdfName(rawdata.p6p15) <- "hgu133aa2cdf"

and see if it works.

HTH,

Jim


> 
>>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 at gskbio.com
> 
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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