Dear Bioconductor Users,

I am trying to find enriched GO terms using topGO. I am using Weight01
algorithm for finding the enrichment.
I get significantly enriched GO Terms but I see an NA value in the expected
column. Below is the code I am
using. Please help me with solving the NA issue.

 sampleGOdata <- new("topGOdata", description = "Simple session", ontology
= "BP",allGenes = geneList, geneSel = topDiffGenes,nodeSize = 10,annot =
annFUN.db,affyLib= "hgu133plus2.db")
resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic =
"fisher")
resultWeight01 <- runTest(sampleGOdata, algorithm ="weight01", statistic =
"fisher")
allRes <- GenTable(sampleGOdata, classicFisher =
resultFisher,weight01=resultWeight01,orderBy = "weight01", ranksOf =
"classicFisher", topNodes = 100,numChar=200)

topDiffGenes <- function(Score) {
  return(Score < 0.05)
}

Thanks,
Kishor

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_SG       LC_NUMERIC=C         LC_TIME=en_SG
 [4] LC_COLLATE=en_SG     LC_MONETARY=en_SG    LC_MESSAGES=en_SG
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C

attached base packages:
 [1] grid      stats4    splines   stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] hgu133plus2.db_2.8.0 org.Hs.eg.db_2.8.0   Rgraphviz_2.2.1
 [4] BiocInstaller_1.8.3  topGO_2.10.0         SparseM_0.96
 [7] GO.db_2.8.0          RSQLite_0.11.2       DBI_0.2-5
[10] AnnotationDbi_1.20.5 Biobase_2.18.0       BiocGenerics_0.4.0
[13] graph_1.36.2         multicore_0.1-7      coin_1.0-21
[16] modeltools_0.2-19    mvtnorm_0.9-9994     survival_2.36-14
[19] samr_2.0             matrixStats_0.6.2    impute_1.32.0

loaded via a namespace (and not attached):
[1] IRanges_1.16.6    lattice_0.20-6    parallel_2.15.1   R.methodsS3_1.4.2
[5] tools_2.15.1

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