[BioC] how can I use the limma result as input in topGo

[Caroline Reiff]

   I wonder if somebody can tell me how I can use my P values from the limma
   test as input into topGo. This is what I tried:
   In topGo I usually do the following using the standard t-test:
   > geneList <- getPvalues(exprs(esetSub), classlabel = y, alternative =
   "two.sided", correction = "BH")
   > geneList[1:10]
       1415670_at    1415671_at    1415672_at    1415673_at  1415674_a_at
   1415675_at
       0.15021513    0.07711458    0.38562825    0.78996178    0.64844312
   0.16257882
   1415676_a_at   1415677_at   1415678_at   1415679_at
     0.92404052   0.01690829   0.30654309   0.55264382
   > length(geneList)
   [1] 9103
   > topDiffGenes <- function(allScore) {
   + return(allScore < 0.01)
   + }
   > GOdata <- new("topGOdata",
   + ontology = "BP",
   + allGenes = geneList,
   + geneSel = topDiffGenes,
   + description = "GO analysis of data. Diff. Expre. between WT and IL10",
   + annot = annFUN.hgu,
   + affyLib = affyLib)
   Building most specific GOs .....        ( 2088 GO terms found. )
   Build GO DAG topology ..........        ( 3286 GO terms and 5438 relations.
   )
   Annotating nodes ...............        ( 6088 genes annotated to the GO
   terms. )
   I tried to replace geneList with the results from limma in the following
   way:
   > geneList<-as.array(mytable$P.Value)
   > dimnames(geneList) <- list(mytable$ID)
   This gives me a genelist just as the one before except that the results are
   ordered by P-value as they come from the limma table
   > geneList[1:10]
          1423677_at NuGO_emt025263_at        1421628_at        1436576_at
        4.335431e-10      2.530289e-09      4.326564e-09      4.470340e-09
          1450034_at        1422632_at        1453080_at        1438037_at
        5.625014e-09      5.931422e-09      6.114187e-09      6.872450e-09
          1422953_at        1446280_at
        1.078998e-08      1.143128e-08
   > length(geneList)
   [1] 9103
   but when I use this as input in topGo I get an error message:
   > topDiffGenes <- function(allScore) {
   + return(allScore < 0.01)
   + }
   > GOdata <- new("topGOdata",
   + ontology = "BP",
   + allGenes = geneList,
   + geneSel = topDiffGenes,
   + description = "WT versus Il10 ko",
   + annot = annFUN.hgu,
   + affyLib = affyLib)
   Error in checkSlotAssignment(object, name, value) :
            assignment of an object of class "AsIs" is not valid for slot
   "allGenes" in an object of class "topGOdata"; is(value, "character") is not
   TRUE
   >
    Hope somebody can help, Many thanks Caroline