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

[Christian.Stratowa@vie.boehringer-ingelheim.com]

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

==============================================
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:
> 
>>library(matchprobes)
>>library(affy) 
>>library(hgu95acdf) 
>>library(hgu95aprobe) 
>>library(hgu95av2cdf) 
> 
> 
> Attaching package: 'hgu95av2cdf'
> 
> 
>         The following object(s) are masked from package:hgu95acdf :
> 
>          i2xy xy2i
> 
> 
>>library(hgu95av2probe)
> 
> 
>>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().

HTH,

Jim



-- 
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