Hi Konika, It is not a "BiomaRt solution", but here is one way you can get this information by using the org.Hs.eg.db package: library(org.Hs.eg.db) get("GO:0003677", org.Hs.egGO2EG) I am sure you can make biomaRt get you this information too if you really want to do it that way. Marc On 12/19/2011 10:48 AM, konika chawla wrote: > Hi, > I want to retrieve all human genes annotated with specific go_ids like > GO:0003677 > > in the listFilters option I see 3 filters - > 1) go- it is giving genes even with other go ids not in the query > 2) with_go and with_go_go giving error that > > Error in getBM(attributes = c("go_id", "name_1006", "entrezgene", "hgnc_symbol", : > biomaRt error: with_go_go is a boolean filter and needs a corresponding logical value of TRUE or FALSE to indicate if the query should retrieve all data that fulfill the boolean or alternatively that all data that not fulfill the requirement should be retrieved. > > > Can you tell what is the difference between the three and which is the best option t be used. > script I used > tf<-read.table("tf_selection_criteria.csv",sep=",",header=TRUE) > library(biomaRt) > mart=useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") > getBM(attributes=c("entrezgene")) > data<-getBM(attributes=c("go_id","go","name_1006","entrezgene","hgnc _symbol","external_gene_id"),filters="go",values=tf[,2], mart=mart) > > Thanks > > Konika Chawla > PhD candidate > Department of Biology > NTNU > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor