Dear list,
I'm using an Hypergeometric Test using hyperGTest from GOstats and 
Category packages. I have several questions related to this issue:

    * What is the usual cutoff value used as an input for the
      hypergeometric test according to the gene set collection used: GO
      BP, GO MF, GO CC, Chromosome Bands, KEGG and PFAM?
    * In the nonspecific filtering, I suppose that one can perform
      different kind of filters depending on the gene set collection
      used. For example, using the nsFilter function:
          o For GO BP: nsFilter(OligoEset,
            require.entrez=TRUE,require.GOBP=TRUE,
            remove.dupEntrez=TRUE,
            var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
            feature.exclude="^AFFX")
          o For GO MF: nsFilter(OligoEset,
            require.entrez=TRUE,require.GOMF=TRUE,
            remove.dupEntrez=TRUE,
            var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
            feature.exclude="^AFFX")
          o For GO CC: nsFilter(OligoEset,
            require.entrez=TRUE,require.GOCC=TRUE,
            remove.dupEntrez=TRUE,
            var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
            feature.exclude="^AFFX")
          o For Chromosome Bands: nsFilter(OligoEset,
            require.entrez=TRUE,require.CytoBand=TRUE,
            remove.dupEntrez=TRUE,
            var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
            feature.exclude="^AFFX")
          o For KEGG: nsFilter(OligoEset, require.entrez=TRUE,
            remove.dupEntrez=TRUE,
            var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
            feature.exclude="^AFFX")

    Therefore, depending on the gene set collection, the filter changes.

    * Once the Hypergeometric Test is done, I don't understand some of
      the fields of the HyperGResult object. What I understood is:
          o ExpCount: the expected number of genes in the selected gene
            list to be found at each tested category term.
          o Count: for each category term tested, the number of genes
            from the interesting gene list that are annotated at the term.
          o Size: for each category term tested, the number of genes
            from the universe gene list that are annotated at the term.
          o OddsRatio: the odds ratio for each category term tested

    If the test is done for over-represented terms, Count is greater
    than ExpCount. Otherwise, the test has been performed for
    under-represented terms. I don't understand the meaning of ExpCount.
    Expected by who?Is it expected a great difference between ExpCount
    and Count? Is there a relationship between ExpCount, Count and the
    p-values? I would like to understand better the meaning of the
    HyperGResult object according to these fields: ExpCount, Count, Size
    and OddsRatio.

Thanks in advance,
Javier


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