goTools problem
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@jorrit-boekel-1993
Last seen 6.8 years ago
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
goTools oligo goTools oligo • 558 views
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Paquet, Agnes ▴ 500
@paquet-agnes-807
Last seen 6.8 years ago
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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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