Hi
I am trying to find ensemble gene ids for the 1372 mouse entrez gene ids  via biomaRt.
but I find different number of genes in result when I do it with biomaRt package compared to BiomaRt online tool.
Strangely online tool gives atleast 10 more genes mapped with ensembl IDs,
The code I use is 

mouse<-read.csv("TFcat_mouse_gene_symbol.txt",sep="\t",header=TRUE)
 ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
  filters = listFilters(ensembl)
attributes = listAttributes(ensembl)
data<-getBM(attributes = c("ensembl_gene_id", "entrezgene"), filters = "entrezgene", values = mouse[,1], mart = ensembl)

Let me know which one is more trustable/ updated?

Konika Chawla
PhD candidate
Department of Biology
NTNU 




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