Abi,

Did you import the package org.Dr.eg.db? Thanks!

library(org.Dr.eg.db)

Best regards,

Julie

On 10/7/11 12:03 PM, "Lakshmanan, Abirami" <Abirami.Lakshmanan@umassmed.edu> wrote:

Hi Julie,

I tried getEnrichedGo term using Ensembl ID/Entrez id and both don’t seem to work.  This is what I did

* installing *source* package ‘org.Dr.eg.db’ ...
> pos5id
[1] "ENSDARG00000055876" "ENSDARG00000042641" "ENSDARG00000026313" "ENSDARG00000052734" "ENSDARG00000070141" "ENSDARG00000057633" "ENSDARG00000012468" "ENSDARG00000043317"
 [9] "ENSDARG00000010008" "ENSDARG00000011317" "ENSDARG00000016319" "ENSDARG00000060260" "ENSDARG00000058631" "ENSDARG00000089730" "ENSDARG00000090914" "ENSDARG00000070903"
[17] "ENSDARG00000060526" "ENSDARG00000010658" "ENSDARG00000006526" "ENSDARG00000000551" "ENSDARG00000022767" "ENSDARG00000056732" "ENSDARG00000089498" "ENSDARG00000057724"
> enrichedGO.dr <- getEnrichedGO (pos5id, feature_id_type="ensembl_gene_id",orgAnn="org.Dr.eg.db", maxP=0.05, multiAdj =TRUE, minGOterm=10,multiAdjMethod="BH")
Error in get(paste(GOgenome, "ENSEMBL2EG", sep = "")) :
  object 'org.Dr.egENSEMBL2EG' not found

SO I converted by Ensembl Id’s to Entrez id ‘s using Biomart and tried similar thing and it seems to fail too.

> posentrz5
[1] "368885"    "334613"    "140599"    "334189"    "100149100" "393984"    "554141"    "321166"    "414331"    "30256"     "559054"    "796384"    "406662"    "100149863"
[15] "140747"    "58050"     "571911"    "777717"    "564095"    "100150664" "100534777" "556200"
> enrichedGO.dr <- getEnrichedGO (posentrz5, feature_id_type="entrez_id",orgAnn="org.Dr.eg.db", maxP=0.05, multiAdj =TRUE, minGOterm=10,multiAdjMethod="BH")
Error in get(paste(GOgenome, "GO", sep = "")) :
  object 'org.Dr.egGO' not found


Am I doing anything wrong.  I read through the Biocunductor list and for yeast genome you asked the user to use orf instead of entrezid.  In my case what do I do?

Thanks,
Abi


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