
Hi Jim,

Thanks for your reply, and you are right, it works as you say ! rma() 
worked fine. A boxplot of the rma expression set looks quite normal.
However, checking the env file with getCdfEnvAffy(), I'm not sure that 
everything is OK :

> getCdfEnvAffy(rawdata.p6p15)
Probe types:
  valid.
XY coordinates:
  22280 invalid probe sets
1007_s_at 1053_at 117_at 121_at 1255_g_at ...
Error in wrapCdfEnvAffy(cdfenv, abatch@nrow, abatch@ncol, abatch@cdfName) 
: 
        invalid CdfEnvAffy

What does that mean ???

Now, for everybody, it seems (at least on my side) that cdfName() can only 
get the name of environment associated with the affybatch, and cannot set 
it. 
I've set it with :
rawdata.p6p15@cdfName <- "hgu133aa2cdf"


Jean-Louis




"James W. MacDonald" <jmacdon@med.umich.edu> 
25-Sep-2006 16:17
 
To
jean-louis.ruelle@gskbio.com
cc
bioconductor@stat.math.ethz.ch
Subject
Re: [BioC] new CDF env from combineAffyBatch is not recognized






Hi Jean-Louis,

jean-louis.ruelle@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@gskbio.com
> 
> 
> 
> The information contained in this message is confidential 
an...{{dropped}}
> 
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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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