Question: GSEABase GOCollection wrong ontology
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gravatar for Hans-Ulrich Klein
10.8 years ago by
United States
Hans-Ulrich Klein330 wrote:
Dear All, I want to generate sets of probes from the affy hgu133plus2 chip from the GO "Molecular Function". I used the GSEABase package: > library("GSEABase") > sets = GeneSetCollection(idType=AnnotationIdentifier("hgu133plus2.db"), setType=GOCollection(ontology="MF")) > sets[[1]] setName: GO:0000002 geneIds: 1557631_at, 202825_at, ..., 203466_at (total: 5) geneIdType: Annotation (hgu133plus2.db) collectionType: GO ids: (0 total) evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND ontology: MF details: use 'details(object)' The Gene Ontology web site says that the id "GO:0000002" belongs to "biological process". Something went wrong... Regards, Hans-Ulrich
ADD COMMENTlink modified 10.8 years ago by Martin Morgan ♦♦ 24k • written 10.8 years ago by Hans-Ulrich Klein330
Answer: GSEABase GOCollection wrong ontology
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gravatar for Martin Morgan
10.8 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
Hans-Ulrich Klein <h.klein at="" uni-muenster.de=""> writes: > Dear All, > > I want to generate sets of probes from the affy hgu133plus2 chip from > the GO "Molecular Function". I used the GSEABase package: > > > library("GSEABase") > > sets = > GeneSetCollection(idType=AnnotationIdentifier("hgu133plus2.db"), > setType=GOCollection(ontology="MF")) > > sets[[1]] > setName: GO:0000002 > geneIds: 1557631_at, 202825_at, ..., 203466_at (total: 5) > geneIdType: Annotation (hgu133plus2.db) > collectionType: GO > ids: (0 total) > evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND > ontology: MF > details: use 'details(object)' > > The Gene Ontology web site says that the id "GO:0000002" belongs to > "biological process". Something went wrong... Hi Hans-Ulrich -- Note that there are 0 id's in collectionType(sets[[1]]). The confusion (some on my part, no doubt) comes from the role that GOCollection plays -- it is meant as a way of representing perhaps several GO ids. The 'ontology' specification filters the ids and creates a collection consisting only of those ids satisfying the ontology. Thus > GOCollection("GO:000002", ontology="MF") collectionType: GO ids: (0 total) evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND ontology: MF > GOCollection(c("GO:0000002", "GO:0000009"), ontology="MF") collectionType: GO ids: GO:0000009 (1 total) evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND ontology: MF > GOCollection(c("GO:0000002", "GO:0000009"), ontology="BP") collectionType: GO ids: GO:0000002 (1 total) evidenceCode: IMP IPI TAS ISS IDA NAS IEA IGI RCA IEP IC NR ND ontology: BP So sets[[1]] contains an empty GOCollection -- the probes form a coherent set based on their GO ids, but there are no GO ids that simultaneously circumscribe the set and satisfy the ontology constraint. Unfortunately, the name of the set is the name of the GO identifier. Probably a more reasonable result is like > sets[ids(GOCollection(names(sets), ontology="MF"))] GeneSetCollection names: GO:0000009, GO:0000010, ..., GO:0060230 (2495 total) unique identifiers: 218444_at, 220865_s_at, ..., 229922_at (31278 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: GOCollection (1 total) At this point it is worth pointing out that evidenceCode behaves differently, removing probes that do not satisfy the evidenceCode constraint. This reflects the fact that the evidence code is not a property of the GO term, but of the geneId. Martin > Regards, > Hans-Ulrich > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
ADD COMMENTlink written 10.8 years ago by Martin Morgan ♦♦ 24k
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