[BioC] About goTools and multiple chips

[Paquet, Agnes]

Dear Radu and Juerg,

At the moment, goTools accepts either probe Ids from a single Affy chip
or GO ids. When using data from different chips, the easiest way to use
goTools is to convert your Affy ids into GO ids, then use these GO ids
as argument (make sure you are using a version of goTools > =1.0.4 as we
found a bug in earlier versions). 

Best,

Agnes



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Radu Dobrin
Sent: Wednesday, February 09, 2005 6:10 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] About goTools and multiple chips

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

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor