Question: goTools: ontoCompare question
12.5 years ago by
firstname.lastname@example.org • 140
email@example.com • 140 wrote:
Hello, I ran ontoCompare on the full list of probes in the mouse4302 genechip both with the default EndNodeList() and with a custom end node list containing only the antioxidant activity, biological_process, cellular_component, and molecular_function GO terms and found what appears to be a discrepency: > length(sviData$svi$ID)  45101 > sviData$svi$ID[1:5]  "1452670_at" "1422340_a_at" "1452114_s_at" "1422644_at" "1423359_at" > listall<-list("allprobes"=sviData$svi$ID) > endlist<-c("GO:0003674", "GO:0005575", "GO:0008150", "GO:0016209") > totalAnnotations<-ontoCompare(listall, probeType="mouse4302", method="none") > write.table(totalAnnotations, file="totalAnnotations.txt") > totalAnnotations2<-ontoCompare(listall, probeType="mouse4302", method="none", endnode=endlist) > write.table(totalAnnotations2, file="totalAnnotations_reduced.txt") When finding the total possible number of annotations for the top level GO terms (BP, MF, CC), I got different numbers for the two approaches, but I got the same numbers for "NotFound" and "antioxidant activity": from totalAnnotations.txt antioxidant activity 127 biological_process 2594 cellular_component 2365 molecular_function 2414 NotFound 11120 ...others from totalAnnotations_reduced.txt antioxidant activity 127 biological_process 28020 cellular_component 28509 molecular_function 30875 NotFound 11120 I was just wondering if anyone knew why this might happen since it affects the interpretation of a comparison I was going to do. These data appear to reflect the histogram output from ontoPlot (so I don't think its an R->txt->excel thing). Is the output with method="none" the total number of times all probes are annotated at the endnode or at a child of the end node? Does it have something to do with the "isa" values in EndNodeList() or my method of creating endlist? R v.2.5.0 goTools v1.8.0 Cheers, Dave --and thank you Dick for recommending topGO. I found what I needed through that package.
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