Question

Annotation of DEXSeqHTML with biomaRt

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Matthew Thornton ▴ 350

@matthew-thornton-5564

Last seen 6 weeks ago

USA, Los Angeles, USC

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??

dexseq biomart • 897 views

ADD COMMENT • link 6.1 years ago Matthew Thornton ▴ 350

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Not sure what is going wrong. Have you tried to include these names by doing the biomart call outside of DEXSeqHTML and then passing the data.frame (where the rownames are the `geneIDs()`) to the extraCols parameter?

ADD REPLY • link 6.0 years ago Alejandro Reyes ★ 1.9k

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I will try this. Can a vector be used with the attributes switch with DEXSeqHTML? Thank you!

ADD REPLY • link 6.0 years ago Matthew Thornton ▴ 350

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Could you post as an answer how you would add annotations using DEXSeqHTML? I would be nice to have more, info, like the descriptions, but I would settle for just the external_gene_names. Could it be that there is not enough room in HTML table?

ADD REPLY • link 6.0 years ago Matthew Thornton ▴ 350

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I don't know if it's just a copy/paste error, but the code you include for setting up biomaRt has a couple of problems. First includeHosts> FALSE should probably be includeHosts = FALSE. Second, the output from listMarts() can't be passed to useDataset(), you want useMart() instead. This should set it up correctly:

placeholder <- useMart(biomart = 'ensembl', 
                       host="http://uswest.ensembl.org")
ensembl <- useDataset("hsapiens_gene_ensembl", mart = placeholder)

ADD REPLY • link 6.0 years ago Mike Smith ★ 6.5k