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biomart / BioMart

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line 3480 did not have 7 elements #8

Open stemangiola opened 5 years ago

stemangiola commented 5 years ago

When I execute this command

# Download symbol list https://wehieduau-my.sharepoint.com/:f:/g/personal/mangiola_s_wehi_edu_au/EganEh5ii4lPthDJWqVH3FAB5Y4xWtjYzFmQeJWcj-Fqgg?e=9Prm6q

load("symbols.RData")
biomaRt::getBM(
    filters=c("hgnc_symbol"),
    values = s, 
    attributes = c(
        'ensembl_gene_id', 
        'entrezgene','hgnc_symbol',
        'description',
        'name_1006',    'namespace_1003', 'definition_1006'
    ),
    mart = biomaRt::useMart("ensembl",dataset="hsapiens_gene_ensembl")
)

I get this error

Batch submitting query [=========================================================================>-------------]  85% eta:  4sError in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 3480 did not have 7 elements

Apparently for no reason.

Thanks