Hi, I would like use ontoCompare on my list of proteins. Then I have retrieved the GO Id for this list. I would like the proportion in my list for BP-rank=1 (proportion in biological adhesion, cell killing ...) To illustrate my problem I take an example: for a protein I can have 2 GO annotations for the BP type. But they can provide from the same parent GO:0008150: Biological process. So there will be a redundance for just one protein. How can I resolve my problem? Thanks a lot Christelle -- Passerelle antivirus IGF --

Hi Christelle, ontoCompare provides several methods for counting the number of GO ids children to a top node. In your case, you can use the TIDS method, which returns the number of children of each node / total number of GO ids describing the group of proteins you provide in input. You can use this method by changing the method aregument to "TIDS" when calling the function: ontoCompare(yourListofGOids,probeType="GO",method="TIDS",goType="BP") Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Christelle Dantec Sent: Thu 8/23/2007 9:13 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] goTools: ontoCompare - GO list Hi, I would like use ontoCompare on my list of proteins. Then I have retrieved the GO Id for this list. I would like the proportion in my list for BP-rank=1 (proportion in biological adhesion, cell killing ...) To illustrate my problem I take an example: for a protein I can have 2 GO annotations for the BP type. But they can provide from the same parent GO:0008150: Biological process. So there will be a redundance for just one protein. How can I resolve my problem? Thanks a lot Christelle -- Passerelle antivirus IGF -- _______________________________________________ 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