[BioC] About goTools and multiple chips

[Radu Dobrin]

Hello all!

Since I have seen many threads about ontoTools and Juerg Straubhaar in 
an e-mail said that :

I tried this:
>ontoCompare(namesList,probeType=c("moe430a","moe430b"),  plot=TRUE)
>[1] "Starting ontoCompare..."
>Error: val;

The reply from John Zhang said that he is missing the moe4302 package. Maybe in his case is true but I have a similar error message when trying my list from moe430 chip. The problem as I see it is that ontoToold DOES NOT accept probeType=c("moe430a","moe430b"), you have to pick either one or the other. 

In my case:

ontoCompare(glists[1],probeType=c("moe430a","moe430b"),plot=T)
[1] "Starting ontoCompare..."
Error: value for "1419791_at" not found
> xx<-as.list(moe430bSYMBOL)
> xx["1419791_at"]
$"1419791_at"
[1] "Zhx3"

As you can see the probe is in the moe430b chip. I think it is a very good idea to modify the code such that it can do GO for both chips. This problem renders ontoTools rather obsolete since one would have to do the GO for each chip separately, merge the output and plot. I would use it... but until the problem is fixed I wrote my own code :)

Radu



-- 
Dr. Radu Dobrin
Department of Molecular Biology
Princeton University
Washington Road
Princeton, NJ 08544-1014
Phone: 609-258-5657
E-mail: rdobrin at molbio.princeton.edu