Entering edit mode
Kishor Tappita
▴
340
@kishor-tappita-2563
Last seen 10.0 years ago
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 value 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