'You must provide a valid Mart object.' using getLDS() Biomart
Entering edit mode
20 months ago
Angelina_G ▴ 10

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 • 1.3k views
Entering edit mode

Ensure you get the latest version of biomaRt BiocManager::install('grimbough/biomaRt')or try at another time as suggested here : Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : Gateway Timeout (HTTP 504).

Entering edit mode

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.


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