   1.

   How do I interpret the result of 'hyperGTest' if the argument
   "testDirection='under'" is supplied? The hypergtest result is given below.
   2.

   Is there a way to find all Entrez IDs associated with a particular GO
   term (For example, GO:0034660).
   3.

   How do I find list of all Entrez IDs which has a GO BP/CC/MF term? My
   gene universe 'uGenes' initially had a total of ~22,000 genes, where as the
   result below show it to be 19,703. This mean that some of my genes in the
   universe did not have an associated GO term. How to find those which were
   left out?



   > library(GOstats)

   > hypTest <- new("GOHyperGParams", ontology = "BP", geneIds = dGenes,
   universeGeneIds = uGenes,

   +                annotation = "org.Mm.eg.db", pvalueCutoff =0.05,
   testDirection='under')

   Warning message:

   In makeValidParams(.Object) : removing geneIds not in universeGeneIds

   > hypRes <- hyperGTest(hypTest)

   > hypRes

   Gene to GO BP  test for under-representation

   10243 GO BP ids tested (13 have p < 0.05)

   Selected gene set size: 575

       Gene universe size: 19703

       Annotation package: org.Mm.eg

   > goRes <- summary(hypRes)

   > dim(goRes)

   [1] 13  7

   > head(goRes)

         GOBPID       Pvalue OddsRatio  ExpCount Count Size
                              Term

   1 GO:0034660 0.0009096559 0.0000000  6.858093     0  235
           ncRNA metabolic process

   2 GO:0006396 0.0012500319 0.2704202 14.212303     4  487
                    RNA processing

   3 GO:0034470 0.0043152380 0.0000000  5.340557     0  183
                  ncRNA processing

   4 GO:0006457 0.0146830925 0.0000000  4.144039     0  142
                   protein folding

   5 GO:0071843 0.0255629678 0.1774194  5.457291     1  187 cellular
   component biogenesis at cellular level

   6 GO:0022613 0.0345792941 0.1897753  5.107090     1  175
    ribonucleoprotein complex biogenesis




-- 
-------------
Mary Kindall
Yorktown Heights, NY
USA

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