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Hi Michaela, You can generate a different endnode list using the function CustomEndNodeList: MFendnode <- CustomEndNodeList("GO:0003674", rank=3) ontoCompare(affylist, probeType="hgu133a", endnode=MFendnode, goType="MF") You can also select endnodes of interest for your project using a GEO browser like Amigo and pass the vector of corresponding GO ids as endnode. Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Michaela G?ndel Sent: Wed 8/29/2007 8:20 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] ontoCompare - 1) notFound 2) GO level Dear list, after downloading data from GEO (which is already GO id annotated) I do a GO analysis using ontoCompare. It all works fine, but the thing I don't understand is why there are so many (around 40%) notFounds. Is the mapping old or how can this happen? I don't believe the GO identifiers are faulty because they come from GEO. Another question is how to limit the GO terms that are output to a certain GO level, eg. 3, because the high-level terms are not very informative. Is it possible to do this in some way, maybe using the endnodelist? Thank you very much in advance, any help is appreciated!! Michaela Guendel R version 2.5.1 (2007-06-27) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: GEOquery goTools GO RMySQL DBI biomaRt RCurl "2.0.5" "1.8.0" "1.16.0" "0.6-0" "0.2-3" "1.10.1" "0.6-0" XML hgug4112a annotate Cairo genefilter survival Biobase "1.9-0" "1.16.0" "1.14.1" "1.3-5" "1.14.1" "2.32" "1.14.0" limma "2.10.5" [[alternative HTML version deleted]] _______________________________________________ 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