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
mouseMart? 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