Question: GetEnrichedGo term
0
gravatar for Julie Zhu
8.0 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
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 [[alternative HTML version deleted]]
yeast biomart • 623 views
ADD COMMENTlink written 8.0 years ago by Julie Zhu4.0k
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