Reporting results of HyperGTest
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@paolo-innocenti-2191
Last seen 6.8 years ago
Hi all, I performed two separate HyperGTest (pkg:GOstats) on different list of DE genes (trt1 vs control and trt2 vs control). The results are good and in the direction I was expecting: I can see from "htmlReport" that the GOterms overrepresented in each list support my hypothesis. My problem now is to "quantify" and to "show" what I can see: I am looking for a nice way to format my results. I have around 50 GO nodes in each list, too many to list them all in two colums. Is there a graphical way (or a compressed table) to show differences in "which branches of the GO" are overrepresented, and possible overlaps? I am basically looking for something in between htmlReport, a DAG graph and the function ontoCompare in goTools. I appreciate any comments on this issue. I have no experience with DAG graph, so if you suggests that it is the way to go, I'd like to be pointed to some documentation (I found GOvis.pdf too confusing as a beginner) Many thanks, Paolo -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden
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@pankaj-chopra-2741
Last seen 6.8 years ago
Might be worth trying 'GOGraph' in the GOstats package. I think I was able to do it using it with the Rgraphviz (?makeNodeAttrs) package. Paolo Innocenti wrote: > Hi all, > > I performed two separate HyperGTest (pkg:GOstats) on different list of > DE genes (trt1 vs control and trt2 vs control). The results are good and > in the direction I was expecting: I can see from "htmlReport" that the > GOterms overrepresented in each list support my hypothesis. > > My problem now is to "quantify" and to "show" what I can see: I am > looking for a nice way to format my results. I have around 50 GO nodes > in each list, too many to list them all in two colums. Is there a > graphical way (or a compressed table) to show differences in "which > branches of the GO" are overrepresented, and possible overlaps? > > I am basically looking for something in between htmlReport, a DAG graph > and the function ontoCompare in goTools. > > I appreciate any comments on this issue. I have no experience with DAG > graph, so if you suggests that it is the way to go, I'd like to be > pointed to some documentation (I found GOvis.pdf too confusing as a > beginner) > > Many thanks, > Paolo > > >
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