Hi,

I have come along a strange behaviour of biomaRt ensembl queries. I get different results when I use the filter "chromosome_name" with values X chromosome and all autosomes or when I use values="*" and then filter for the same chromosomes.

ensembl.new <- useMart("ENSEMBL_MART_ENSEMBL",host="may2015.archive.ensembl.org")
ensemblmmusculus.new = useDataset("mmusculus_gene_ensembl",mart=ensembl.new)
chromosome.input <- getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"), filter="chromosome_name", value=c("X",as.character(1:19)), mart=ensemblmmusculus.new)
all.input <- getBM(attributes = c("ensembl_gene_id", "ggallus_homolog_orthology_type", "ggallus_homolog_orthology_confidence","ggallus_homolog_chromosome", "chromosome_name"),  value="*", mart=ensemblmmusculus.new)
all.input <- filter(all.input,chromosome_name %in% c("X",as.character(1:19)))


length(unique(chromosome.input$ensembl_gene_id))

[1] 26708
length(unique(all.input$ensembl_gene_id))

[1] 43625

In principle I thought both queries should yield the same result. Does someone know what's wrong here?