Hi All,

I am using 'GoStat' package for GO enrichment analysis and so far I have been able to generate results from 'hyperGTest' without any issue. Here is my dummy code:

top.genes = read.delim("Top200_others.txt")

## Test set ###########
entrezTest.AF = top.genes[[1]] ## ENTREZ IDs

## Background set #######
all.genes = keys(org.Mm.eg.db, keytype="SYMBOL");all.genes[1:5] ## Using all genes as background
entrezUniverse.AF = select(org.Mm.eg.db,as.character(all.genes),
columns= "ENTREZID",keytype = "SYMBOL")
b = entrezUniverse.AF[[2]] ## Select the Entrez ids
b <- b[!is.na(b)];length(b)

## Perform Test ##########
hgCutoff <- 0.005
params <-
new("GOHyperGParams",geneIds=entrezTest.AF,universeGeneIds=b,annotation="org.Mm.eg.db",
ontology="BP",pvalueCutoff=hgCutoff,conditional=FALSE,testDirection="over")
paramsCond <- params
conditional(paramsCond) <- TRUE
hgOver <- hyperGTest(params)

## Write Results ########
htmlReport(hgOver, file=paste("IL_Mand_RClustGO2",".html",sep=""))

Now all I need is the list of test genes under enriched go categories. For Ex:

GOBPID    Pvalue    OddsRatio    ExpCount    Count    Size    Term
GO:0009888    0.000    5.988    9    41    1449    tissue development
GO:0009887    0.000    7.597    5    30    789    organ morphogenesis

Which test genes (entrez ids) were present in 'tissue developemnt'? Is is possible?

Thanks in Advance

AK

The following code gives the Entrez IDs of all genes associated with "tissue development".

library(org.Mm.eg.db)
x <- org.Mm.egGO2ALLEGS
keys(x) <- "GO:0009888"
mappedLkeys(x)

Hi Atul,

See ?probeSetSummary. You can also use ReportingTools to create a nicer version of the HTML table you have made, but with links to sub-tables that contain the significant genes that caused that term to be significant (see
pages 4-5 in the ReportingTools basics vignette

http://bioconductor.org/packages/release/bioc/vignettes/ReportingTools/inst/doc/microarrayAnalysis.pdf ).

Best,

Jim

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099