Question: bioMart can't connect cosmicMart
0
gravatar for callmevvs
2.8 years ago by
callmevvs0
France
callmevvs0 wrote:

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 beacuse of the new modul "login" in COSMIC, does someone know the reason?

wenjun

R • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Neilfws46k • written 2.8 years ago by callmevvs0
1
gravatar for Neilfws
2.8 years ago by
Neilfws46k
Sydney, Australia
Neilfws46k wrote:

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

 

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Neilfws46k

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 ....

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by callmevvs0

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.

ADD REPLYlink written 2.8 years ago by Neilfws46k
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