[BioC] Error with CDF environment when using combineAffyBatch of package matchprobes

Christian.Stratowa@vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Wed Mar 8 16:04:44 CET 2006

Dear James

Thank you, this seems to be indeed the case. What I did was:
>comb95cdf <- res$cdf

Meanwhile a colleague told me to add:
>res$dat at cdfName <- "comb95"
and this solved the problem, too.

Best regards

Christian Stratowa, PhD
Boehringer Ingelheim Austria
Dept NCE Lead Discovery - Bioinformatics
Dr. Boehringergasse 5-11
A-1121 Vienna, Austria
Tel.: ++43-1-80105-2470
Fax: ++43-1-80105-2782
email: christian.stratowa at vie.boehringer-ingelheim.com

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Wednesday, March 08, 2006 15:51
To: Stratowa,Dr.,Christian FEX BIG-AT-V
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error with CDF environment when using
combineAffyBatch of package matchprobes

Christian.Stratowa at vie.boehringer-ingelheim.com wrote:
> Hi,
> I would like to combine U95A and U95Av2 files for RMA, and tried to 
> use function combineAffyBatch of package matchprobes (version 1.2.1) 
> as described in the
> vignette:
> Attaching package: 'hgu95av2cdf'
>         The following object(s) are masked from package:hgu95acdf :
>          i2xy xy2i
>>x95A <- ReadAffy(celfile.path="HG-U95A")
>>x95Av2 <- ReadAffy(celfile.path="HG-U95Av2") 
>>res <- combineAffyBatch(list(x95A,x95Av2),
> c("hgu95aprobe","hgu95av2probe"), newcdf="comb95") 
> package:hgu95aprobe     hgu95aprobe 
> package:hgu95av2probe   hgu95av2probe 
> 197193 unique probes in common
> Here is what Iget when doing RMA:
>>dat.rma <- rma(res$dat)

I think you missed a step here. You have to point to the cdfenv to use. 
 From the vignette:

comb <- res$cdf     <-- This puts the correct cdfenv into your

.GlobalEnv so rma() can find it.
z <- rma(res$dat)

So I think you need to add

comb95 <- res$cdf

before your call to rma().



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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