Dear list,

I am making a get set enrichment analysis, my commands are :

library(biomaRt)

 #list to test
broilers_HT.test<- broilers_HT$entrezgene
#now I define my universe as all the entrezgenes
all <- total_data_u$entrezgene
# in your case, it's not all the entrezgenes, but those corresponding to the
ensembl_gene_id included in your analysis
# if you have problem with this, contact me then



# now the regular GOstats testing
library(GOstats)
library(multtest)
library(org.Hs.eg.db)

ont = c("BP")
options(digits=3)

params_temp = new("GOHyperGParams", geneIds= broilers_HT.test,
universeGeneIds=all,
                    annotation="org.Hs.eg.db", ontology=ont,
                    pvalueCutoff=1, conditional = TRUE,
                    testDirection = "over")
hGT = hyperGTest(params_temp)
#ps1 <- probeSetSummary(hGT, 0.05, 5)
result <- summary(hGT)
pval  = result$Pvalue                 ## add FDR info
library(multtest)
FDRpval = mt.rawp2adjp( pval , c("Bonferroni","BH", "BY"))
GO.resultbroilers_HT2 <- cbind(result,FDRpval$adjp)

this has worked well before and now I am getting the following error:

Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :    value for
"GO:0010817" not found

the difference is that I have updated my linux distribution, befor I had
Unbuntu 9.04 and now I have 9.10 and after that I had to reinstall all the
bioconductor packages, like biomart GOstats, multtest and org.Hs.eg.db

can someone help me?

thanks
Andreia

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