Entering edit mode
Voke AO
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760
@voke-ao-4830
Last seen 9.6 years ago
My apologies. I omitted the "error" in my initial post.
Hi all,
I ran a list of genes through biomaRt with the following code and it
gives me this error in the snp retrieval aspect of it. I doubt it's a
connection/proxy problem because I have that taken care of, I think
and every step prior to that seemed to have worked just fine.
Any ideas what the problem might be?
Thanks.
-Avoks
mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
genes = read.delim("DAVID_BFE_Genes_4_06_2012.txt", header = TRUE)
results = getBM(attributes = c("ensembl_gene_id", "hgnc_symbol",
"chromosome_name","strand", "transcript_start", "transcript_end" ),
filters = "hgnc_symbol", values = genes$Symbol, mart = mart)
mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
results2 = getBM(attributes = c("refsnp_id", "allele", "snp",
"chrom_strand", "cds_start","cds_end","validated",
"consequence_type_tv","phenotype_name"),
filters = "ensembl_gene", values = results$ensembl_gene_id,
mart = mart2)
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