[BioC] goTools problem

[Paquet, Agnes]

Hi Jorrit,
 
Your command is correct, but goTools does not support Operon Rat arrays unfortunately. It will work only for Human or Mouse arrays. One way around this problem would be to retrieve the GO ids for your oligos using another source on the web (they may also be included with the annotations provided by Operon), and then use the GO ids in goTools.
 
Best,
 
Agnes

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of Jorrit Boekel
Sent: Thu 1/11/2007 2:20 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] goTools problem



Dear all,

I want to use goTools to show gene ontologies of my two-color array
data, which contains Rat Operon IDs (V3.0). My output is however the
following:

>ontoCompare(testid4, probeType="operon", plot=TRUE)
[1] "Starting ontoCompare..."
[1] 60160     2
[1] "Number of lists = 1"
Error in as.vector(x, mode) : invalid argument 'mode'

When I run the example operonlist included in the package through
ontoCompare it works fine, so I figure there is something wrong with my
list. It looks like this

$L1
 [1] "Rn30010572" "Rn30009669" "Rn30020616" "R001191_01"  etc...

When I substitute my rat data by one of the package's operon-IDs, it
again works. Is there maybe something wrong with my oligo notation?

Cheers,
jorrit

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