hello: In my previous question I asked about hyperGTest and Fishers exact test. I do not know if any functions are available to do fishers exact test in bioconductor. I am trying using a sample code given as an example, which appears mostly deprecated. #### reprinted from JSM2005 James Wettenhall. August 6-7, 2005 lab session#### Here estrogen dataset was used. library(hgu95av2) geneIDs <- ls(hgu95av2cdf) LocusLinkIDs <- as.character(unlist(lapply(mget(geneIDs,env=hgu95av2LOCUSID), function LL.ID) { returnpasteLL.ID,collapse="; ")) } ))) topLocusLinkIDs <- LocusLinkIDs[top50.Est10] topLocusLinkIDs <- topLocusLinkIDs[topLocusLinkIDs!="NA"] library(GOstats) goHyperG <- GOHyperG(unique(topLocusLinkIDs), lib="hgu95av2", what="MF") # MF is an abbreviation for "Molecular Function". # See ?GOHyperG for more information. names(goHyperG) bestGOs <- goHyperG$pvalues[goHyperG$pvalues < 0.2] Now that GOHyperG is deprecated, I tried to modify the code and I do not understand entrezUniverse. How entrezUniverse can be obtained for this estrogen example dataset. ###### Modification according to new hyperGTest: library(GOstats) gparams <- new("GOHyperGParams", geneIDs = topLocusLinkIDs, universeGeneIDs = entrezUniverse, annotation="hgu95av2",ontology='MF',pvalueCutoff = hgCutoff, conditional =FALSE, testDirection = "over") hgOver <- hyperGTest(gparams) Can some one help me please, of hot to get entrezUniverse for Estrogen dataset. Thanks ________________________________________________________________ ____________________ Be a better pen pal.

Hi Srinivas, There is a vignette in the GOstats package that shows how to do what you ask. However, it is slightly easier these days if you use one of the new SQLite annotation packages. > library(hgu95av2.db) > library(GOstats) > hasGO <- toTable(hgu95av2GO)[,1] > univ <- unique(getEN(prbs, "hgu95av2")) Note that you also want to choose only those probesets in your significant set that both have GO symbols appended, and have Entrez Gene IDs. Say myprbs is a vector of interesting probeset IDs: > hasGOprbs <- myprbs[myprbs %in% hasGO] > geneIds <- getEN(hasGOprbs, "hgu95av2") > geneIds <- geneIds[!duplicated(geneIds)] > param <- new("GOHyperGParams", geneIds=geneIds, universeGeneIds=univ, annotation="hgu95av2", ontology="MF", conditional=TRUE) > hypt <- hyperGTest(param) Note: typed from memory and not tested since I don't have R on my home comp right now, and there may be typos since this cat keeps wanting attention ;-D Best, Jim Srinivas Iyyer wrote: > hello: > > In my previous question I asked about hyperGTest and > Fishers exact test. I do not know if any functions > are available to do fishers exact test > in bioconductor. > > > I am trying using a sample code given as an example, > which appears mostly deprecated. > > > > > #### reprinted from JSM2005 James Wettenhall. August > 6-7, 2005 lab session#### > > Here estrogen dataset was used. > > > > library(hgu95av2) > geneIDs <- ls(hgu95av2cdf) > LocusLinkIDs <- > as.character(unlist(lapply(mget(geneIDs,env=hgu95av2LOCUSID), > function LL.ID) { return(pasteLL.ID,collapse="; > ")) } ))) > topLocusLinkIDs <- LocusLinkIDs[top50.Est10] > topLocusLinkIDs <- > topLocusLinkIDs[topLocusLinkIDs!="NA"] > > library(GOstats) > goHyperG <- GOHyperG(unique(topLocusLinkIDs), > lib="hgu95av2", what="MF") > # MF is an abbreviation for "Molecular Function". > # See ?GOHyperG for more information. > names(goHyperG) > bestGOs <- goHyperG$pvalues[goHyperG$pvalues < 0.2] > > > > > > Now that GOHyperG is deprecated, I tried to modify the > code and I do not understand entrezUniverse. > How entrezUniverse can be obtained for this estrogen > example dataset. > > > ###### > Modification according to new hyperGTest: > > library(GOstats) > gparams <- new("GOHyperGParams", geneIDs = > topLocusLinkIDs, universeGeneIDs = entrezUniverse, > annotation="hgu95av2",ontology='MF',pvalueCutoff = > hgCutoff, conditional =FALSE, testDirection = "over") > > hgOver <- hyperGTest(gparams) > > Can some one help me please, of hot to get > entrezUniverse for Estrogen dataset. > > Thanks > > > ______________________________________________________________ ______________________ > Be a better pen pal. > > _______________________________________________ > 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 >