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

[James W. MacDonald]

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