Hello! I am trying to annotate the output of DEXSeqHTML for ease of my collaborators. I am using the code but not getting any annotation. Does anyone else have this problem?
DEXSeqHTML(dxr1, genes=NULL, path="DEXSeqReport", file="testForDEU.html", fitExpToVar="condition", FDR=0.1, color=NULL, color.samples=NULL, mart="ensembl", filter="ensembl_gene_id_version", attributes=c("ensembl_gene_id","external_gene_name","description"), extraCols=NULL)
I set up the biomaRt "ensembl" with the following
placeholder <- listMarts(mart = NULL, host="http://uswest.ensembl.org", path="/biomart/martservice", port=80, includeHosts> FALSE, archive = FALSE, ssl.verifypeer = TRUE,ensemblRedirect = TRUE, verbose = FALSE) ensembl = useDataset("hsapiens_gene_ensembl", mart=placeholder) > ensembl Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the hsapiens_gene_ensembl dataset>
If I use getBM with the same filters and attributes and the ensembl gene id's with version, I get the output. Any suggestions??