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.
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).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 ismartL
. That suggests it's a problem with thing being passed to themartL
argument.