"Size" in summary() of "hyperGTest()

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Sergei Manakov ▴ 30

@sergei-manakov-3292

Last seen 10.3 years ago

Hello, I assume that "Size" column in the table generated by summary() of "GOHyperGResult" object produced by hyperGTest() function from "GOstats" package is the total size of a given GO category. In this regard I am puzzled why values in this field are slightly different for the same GO categories when I run the hyperGTest() on different query gene lists, even when using the same Universe. I would be grateful for any suggestions. thanks, Sergei

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ADD COMMENT • link updated 15.9 years ago by rgentleman ★ 5.5k • written 15.9 years ago by Sergei Manakov ▴ 30

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.7 years ago

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Hi Sergei, Sorry to be so slow in getting back to you. On Tue, Feb 17, 2009 at 3:40 AM, Sergei Manakov <manakov at="" ebi.ac.uk=""> wrote: > Hello, > > I assume that "Size" column in the table generated by summary() of > "GOHyperGResult" object produced by hyperGTest() function from > "GOstats" package is the total size of a given GO category. Not necessarily, it will depend on a number of factors (some of them depend on parameters you have set). So, first, it does depend on the gene universe, but it also will vary if you have set conditional=TRUE, as in that case any significant children are excluded - which is what conditional means, in this setting. I believe you will find that they are always identical if you set conditional=FALSE, but please let me know if not, and in that case, if you could follow the posting guide and provide details such as sessionInfo() and a small example, I can try to be more helpful. best wishes Robert > > In this regard I am puzzled why values in this field are slightly > different for the same GO categories when I run the hyperGTest() on > different query gene lists, even when using the same Universe. > > I would be grateful for any suggestions. > > thanks, > Sergei > > _______________________________________________ > 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 > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

ADD COMMENT • link 15.9 years ago rgentleman ★ 5.5k

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Hello Robert, Thanks for your reply. You are right, indeed I have used conditional = TRUE, and that is the reason why "Size" differs. Sorry about that, I should have guessed that myself. However, I find the description of the option "conditional" rather short in the Vignette. Could you please maybe just in a few sentences explain what it exactly it does? That would be very helpful. thanks, Sergei 2009/2/18 Robert Gentleman <rgentlem at="" fhcrc.org="">: > Hi Sergei, > Sorry to be so slow in getting back to you. > > On Tue, Feb 17, 2009 at 3:40 AM, Sergei Manakov <manakov at="" ebi.ac.uk=""> wrote: >> Hello, >> >> I assume that "Size" column in the table generated by summary() of >> "GOHyperGResult" object produced by hyperGTest() function from >> "GOstats" package is the total size of a given GO category. > > Not necessarily, it will depend on a number of factors (some of them > depend on parameters you have set). > So, first, it does depend on the gene universe, but it also will > vary if you have set conditional=TRUE, as in that case any significant > children are excluded - which is what conditional means, in this > setting. I believe you will find that they are always identical if > you set conditional=FALSE, but please let me know if not, and in that > case, if you could follow the posting guide and provide details such > as sessionInfo() and a small example, I can try to be more helpful. > > best wishes > Robert >> >> In this regard I am puzzled why values in this field are slightly >> different for the same GO categories when I run the hyperGTest() on >> different query gene lists, even when using the same Universe. >> >> I would be grateful for any suggestions. >> >> thanks, >> Sergei >> >> _______________________________________________ >> 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 >> >> > > > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org >

ADD REPLY • link 15.9 years ago Sergei Manakov ▴ 30

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* On 2009-02-19 at 00:54 +0000 Sergei Manakov wrote: > Thanks for your reply. You are right, indeed I have used conditional = > TRUE, and that is the reason why "Size" differs. Sorry about that, I > should have guessed that myself. However, I find the description of > the option "conditional" rather short in the Vignette. Could you > please maybe just in a few sentences explain what it exactly it does? > That would be very helpful. The help page for GOstats::hyperGTest has some detail: When 'conditional(p) == TRUE', the 'hyperGTest' function uses the structure of the GO graph to estimate for each term whether or not there is evidence beyond that which is provided by the term's children to call the term in question statistically overrepresented. The algorithm conditions on all child terms that are themselves significant at the specified p-value cutoff. Given a subgraph of one of the three GO ontologies, the terms with no child categories are tested first. Next the nodes whose children have already been tested are tested. If any of a given node's children tested significant, the appropriate conditioning is performed. You might also find some of the discussion in this paper helpful: > citation("GOstats") To cite GOstats in publications use: S Falcon and R Gentleman. Using GOstats to test gene lists for GO term association. Bioinformatics, 23(2):257-8, 2007. + seth -- Seth Falcon | http://userprimary.net/user/

ADD REPLY • link 15.9 years ago Seth Falcon ▴ 150

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