Entering edit mode
Jared J. Bisogni
▴
10
@jared-j-bisogni-1284
Last seen 9.6 years ago
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