[BioC] Error with CDF environment when using combineAffyBatch of pac kage matchprobes - mas5

Thu Mar 9 09:52:23 CET 2006

After adding 
>comb95 <- res$cdf 
rma normalization works well when using rma() or expresso(). 

Sorrowly, mas5 does not work, neither mas5() nor expresso(), in both cases I
get the error: 
>dat.mas <- mas5(res$dat) 
background correcting...Error in as.vector(data) : NAs in foreign function
call (arg 2) 
In addition: Warning message: 
NAs introduced by coercion 

Of course, mas5 can be calculated separately for U95A and U95Av2, but it
would be nice, if it could also be used with the combined affybatch.

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:   Stratowa,Dr.,Christian FEX BIG-AT-V  
Sent:   Wednesday, March 08, 2006 15:06 
To:     'bioconductor at stat.math.ethz.ch' 
Subject:        Error with CDF environment when using combineAffyBatch of
package matchprobes 

	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) 
Warning: unable to access index for repository
<http://bioconductor.org/packages/bioc/1.7/src/contrib>
http://bioconductor.org/packages/bioc/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/omegahat/1.7/src/contrib>
http://bioconductor.org/packages/omegahat/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/lindsey/1.7/src/contrib>
http://bioconductor.org/packages/lindsey/1.7/src/contrib 
Warning: unable to access index for repository
<http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered: 
Specified environment does not contain comb95 
Library - package comb95cdf not installed 
Data for package affy did not contain comb95cdf 
Bioconductor - comb95cdf not available 

	Here is what I get for "res": 
> res 
$dat 
Warning: unable to access index for repository
<http://bioconductor.org/packages/bioc/1.7/src/contrib>
http://bioconductor.org/packages/bioc/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/omegahat/1.7/src/contrib>
http://bioconductor.org/packages/omegahat/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/lindsey/1.7/src/contrib>
http://bioconductor.org/packages/lindsey/1.7/src/contrib 
Warning: unable to access index for repository
<http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered: 
Specified environment does not contain comb95 
Library - package comb95cdf not installed 
Data for package affy did not contain comb95cdf 
Bioconductor - comb95cdf not available 
AffyBatch object 
size of arrays=0x0 features (12328 kb) 
cdf=comb95 (??? affyids) 
number of samples=4 
Warning message: 
missing cdf environment ! in: show(list()) 
Warning: unable to access index for repository
<http://bioconductor.org/packages/bioc/1.7/src/contrib>
http://bioconductor.org/packages/bioc/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/annotation/1.7/src/contrib>
http://bioconductor.org/packages/data/annotation/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/data/experiment/1.7/src/contrib>
http://bioconductor.org/packages/data/experiment/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/omegahat/1.7/src/contrib>
http://bioconductor.org/packages/omegahat/1.7/src/contrib 
Warning: unable to access index for repository
<http://bioconductor.org/packages/lindsey/1.7/src/contrib>
http://bioconductor.org/packages/lindsey/1.7/src/contrib 
Warning: unable to access index for repository
<http://cran.fhcrc.org/src/contrib> http://cran.fhcrc.org/src/contrib 
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered: 
Specified environment does not contain comb95 
Library - package comb95cdf not installed 
Data for package affy did not contain comb95cdf 
Bioconductor - comb95cdf not available 

	It seems that the newly created CDF environment is not recognized. 
Does anyone know what might be the reason and how to solve this problem? 

	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