R help - Jan 2010 - combine 3 affybatches

Hello,

Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array)
Im useing this script:

library(matchprobes)
library(affy)
library(AnnotationDbi)
library(hgu133plus2probe)
library(hgu133aprobe)
library(hgu133a.db)

u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch
u133a1 = ReadAffy() # reading hgu133a cel file into affybatch
u133a2 = ReadAffy() # reading hgu133a cel file into affybatch

data<-combineAffyBatch(list(u133p2,u133a1,u133a2),c("hgu133plus2probe","hgu133aprobe","hgu133aprobe"),newcdf="mycdf")

This wil give the following error:

package:hgu133plus2probe        hgu133plus2probe        
package:hgu133aprobe    hgu133aprobe    
241837 unique probes in common
Error in as.vector(x, "character") : 
  cannot coerce type 'closure' to vector of type 'character'

Can somebody help me with the combining of 3 affybatches?

Joeri Meijsen
TU Delft the Netherlands
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On 29.01.2010 11:44, joez wrote:
>
> Hello,
>
> Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array)
> Im useing this script:
>
> library(matchprobes)
> library(affy)
> library(AnnotationDbi)
> library(hgu133plus2probe)
> library(hgu133aprobe)
> library(hgu133a.db)
>
> u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch
> u133a1 = ReadAffy() # reading hgu133a cel file into affybatch
> u133a2 = ReadAffy() # reading hgu133a cel file into affybatch
>
>
data<-combineAffyBatch(list(u133p2,u133a1,u133a2),c("hgu133plus2probe","hgu133aprobe","hgu133aprobe"),newcdf="mycdf")
>
> This wil give the following error:
>
> package:hgu133plus2probe        hgu133plus2probe
> package:hgu133aprobe    hgu133aprobe
> 241837 unique probes in common
> Error in as.vector(x, "character") :
>    cannot coerce type 'closure' to vector of type
'character'
>
> Can somebody help me with the combining of 3 affybatches?
>
> Joeri Meijsen
> TU Delft the Netherlands
I'd suggest to ask this on the BioC mailing list ...

Uwe Ligges