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 




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