[BioC] Fishers Exact test, hyperGTest - GO analysis ... contd..

[Srinivas Iyyer]

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(paste(LL.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


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