[BioC] problem with combineAffyBatch

[Jared J. Bisogni]

Hello,
I have been trying to combine data from rgu34a and rtu34 chips using
‘combineAffyBatch’ from the package matchprobes.  My problem is that the
resulting AffyBatch object has array sizes of 0x0. I am running version
2.1.0 of R for windows and have version 1.0.22 of matchprobes.

Here is my code:


pd1<-new("phenoData",pData=data.frame(id="ny"), varLabels=list("phenovar"))
pd2<-new("phenoData",pData=data.frame(id="ge"), varLabels=list("phenovar"))

> x1<-read.affybatch(file1,compress=TRUE, phenoData=pd1)
> x2<-read.affybatch(file2,compress=TRUE, phenoData=pd2)

comb<-combineAffyBatch(list(x1,x2),c("rgu34aprobe","rtu34probe"),
	"newset",verbose=TRUE)

package:rgu34aprobe     rgu34aprobe
package:rtu34probe      rtu34probe
16612 unique probes in common

  Here is what I get

>comb
$dat
AffyBatch object
size of arrays=0x0 features (523 kb)
cdf=newset (1036 affyids)
number of samples=2
number of genes=1036
annotation=

$cdf
<environment: 074EDC14>

What can I do to fix this?
Jared