Hi all,
 
I'm running globaltest on 2 sets of 6 Rat 230 2.0 chips. 
 
When I run 
 
> kegg <- as.list(rat2302PATH2PROBE)
> gt.kegg <- globaltest(x.gcrma, "state", kegg)
 
to generate a gt result of kegg pathways and associated P values (where
x.gcrma is my eset), everything works fine.
 
When I run
 
> go <- as.list(rat2302GO2ALLPROBES)
> gt.go <- globaltest(x.gcrma, "state", go)
 
I get the following error:
Error in cbind(deparse.level, ...) : number of rows of matrices must
match (see arg 2)

The go list looks like this:
> go[1:5]
$`GO:0004816`
named character(0)
 
$`GO:0051103`
         ISS 
"1367676_at" 
 
$`GO:0004817`
named character(0)
 
$`GO:0045943`
         IMP 
"1372564_at" 
 
$`GO:0006260`
         ISS          TAS          TAS          NAS          TAS
ISS 
"1367676_at" "1387644_at" "1387795_at" "1388182_at" "1388744_at"
"1394003_at" 
         NAS          ISS          ISS          TAS          ISS
ISS 
"1388911_at" "1370046_at" "1389090_at" "1367941_at" "1367676_at"
"1387120_at" 
         ISS          ISS          ISS          IMP          ISS
ISS 
"1391703_at" "1398790_at" "1367827_at" "1371911_at" "1389090_at"
"1385056_at" 

any ideas?
 
Thanks
 
Tarun Nayar
Genome Sciences Centre, BC, Canada
 
 

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