I have a list of transcript ids of gasterosteus aculeatus for which I need to extract the gene names, descriptions and other annotations from biomart. While I am using biomaRt R package and the getBM function I am getting the following error
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND
It seems that newest versions of biomaRt package cannot run.
My script is as follows
ensembl=useMart(biomart="ensembl",dataset="gaculeatus_gene_ensembl") TSS25p_D_Ens = getBM(attributes = c('ensembl_gene_id','ensembl_transcript_id','chromosome_name','start_position','end_position','go_id','go_linkage_type'), filters = 'ensembl_transcript_id', values = TSS25p_D_geneID, mart = ensembl)
The TSS25p_D_Ens file has the ensembl transcripts ID for the species and looks like this:
> TSS25p_D_geneID []  "ENSGACT00000010774" []  "ENSGACT00000016763" []  "ENSGACT00000022831" > ensembl Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the gaculeatus_gene_ensembl dataset
Because I cannot understand what I am running wrong could someone help?
Thank you in advance. Arun