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'You must provide a valid Mart object.' using getLDS() Biomart

Hello, I have a list of gene names from mouse and was trying to get the list of homolog genes from human.

I tried to use Biomart, however I encountered problems in connecting to the site and creating Mart object.

I want to run the following:

mylist = getLDS(
   mart <- human,
   attributes = c('ensembl_gene_id','external_gene_name','chromosome_name'),
   martL <- mouse,
   attributesL = c('mgi_symbol','ensembl_gene_id','chromosome_name','gene_biotype'),
   filters = 'external_gene_name',
   values = PCD$external_gene_name)

If I try human <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensembl') or human <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl', host="https://asia.ensembl.org") or human <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensembl', mirror = "asia") I get:

Error in martCheck(martL) : 
  You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.

If I try useMart('ensembl', dataset = 'hsapiens_gene_ensembl') I get:

Ensembl site unresponsive, trying useast mirror
Error in bmRequest(request = request, httr_config = martHTTRConfig(mart),  : 
  Gateway Timeout (HTTP 504).

I don't really get why and didn't really find solutions to You must provide a valid Mart object by google...

Thank you for your help.

ensembl biomart
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updated by Mike Smith Mike Smith • written by Angelina_G • Angelina_G

How are you defining the mouse Mart? If you notice from the error message is says "Error in martCheck(martL)", where the important part here is martL. That suggests it's a problem with thing being passed to the martL argument.

• 0 views • link
written by Mike Smith Mike Smith

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