bioMart can't connect cosmicMart

Question

[callmevvs]

Hello everyone, I'm a new R user. Today afternoon I've got a error of useMart command:

> cosmicName=useMart("CosmicMart",host="cancer.sanger.ac.uk")

Opening and ending tag mismatch: meta line 6 and head
Opening and ending tag mismatch: input line 77 and dd
Opening and ending tag mismatch: input line 83 and dd
Opening and ending tag mismatch: input line 89 and dd
Opening and ending tag mismatch: dd line 88 and dl
Opening and ending tag mismatch: dd line 82 and form
Opening and ending tag mismatch: dd line 76 and div
EntityRef: expecting ';'
EntityRef: expecting ';'
Opening and ending tag mismatch: dl line 72 and div
Opening and ending tag mismatch: form line 71 and div
Opening and ending tag mismatch: br line 132 and div
Opening and ending tag mismatch: br line 126 and body
Opening and ending tag mismatch: div line 114 and html
Premature end of data in tag div line 70
Premature end of data in tag div line 68
Premature end of data in tag div line 67
Premature end of data in tag div line 22
Premature end of data in tag body line 21
Premature end of data in tag head line 1
Premature end of data in tag html line 1
Error: 1: Opening and ending tag mismatch: meta line 6 and head
2: Opening and ending tag mismatch: input line 77 and dd
3: Opening and ending tag mismatch: input line 83 and dd
4: Opening and ending tag mismatch: input line 89 and dd
5: Opening and ending tag mismatch: dd line 88 and dl
6: Opening and ending tag mismatch: dd line 82 and form
7: Opening and ending tag mismatch: dd line 76 and div
8: EntityRef: expecting ';'
9: EntityRef: expecting ';'
10: Opening and ending tag mismatch: dl line 72 and div
11: Opening and ending tag mismatch: form line 71 and div
12: Opening and ending tag mismatch: br line 132 and div
13: Opening and ending tag mismatch: br line 126 and body
14: Opening and ending tag mismatch: div line 114 and html
15: Premature end of data in tag div line 70
16: Premature end of data in tag div line 68
17: Premature end of data in tag div line 67
18: Premature end of data in tag div line 22
19: Premature end of data in tag body line 21
20: Premature end of data in

The command worked before. I don't know if it's because of the new module "login" in COSMIC, does someone know the reason?

wenjun

Answer 1

[Neilfws]

Just omit the host parameter.

library(biomaRt)

marts <- listMarts()
marts[grep("cosmic", marts$biomart, ignore.case = T), ]
#       biomart            version
# 26 CosmicMart COSMIC (SANGER UK)

mart.cosmic <- useMart("CosmicMart")
listDatasets(mart.cosmic)
#    dataset description version
# 1 COSMIC67    COSMIC67
# 2 COSMIC68    COSMIC68
# 3 COSMIC66    COSMIC66

[callmevvs]

thanks Neilfws, but in defaut host there is no data for cosmic ....

> cosmicSet
Object of class 'Mart':
 Using the CosmicMart BioMart database
 Using the COSMIC68 dataset

>atrib
[1] "id_sample"         "gene_name"         "samp_gene_mutated"

> cosmicTable=getBM(attributes=atrib,mart=cosmicSet)
> cosmicTable
[1] id_sample         gene_name         samp_gene_mutated
<0 rows> (or 0-length row.names)

nothing ....

[Neilfws]

Interesting. Well, no data are returned using the BioMart web interface either, so the issue is not R/biomaRt. Maybe the issue is the login requirement, as you say.