Hi Robin,
I am using the new email system here at UofT but thanks for forwarding the
email to me.
I tried using the attribute name "referencedatabase_ncbi_gene" but it gave
me the following error message. Please let me know if I need a certain
version of biomaRt for my query to work or if there is another name for the
attribute (the output of listAttributes(mart) still lists
"referencedatabase_entrez_gene" and there is no mention of ncbi anywhere).
I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29).
Command and Error:
> entrezids =
getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_list",
values=c(pathwayids[1]), mart=mart)
Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters =
"pathway_id_list", :
Invalid attribute(s): referencedatabase_ncbi_gene
Please use the function 'listAttributes' to get valid attribute names
Thanks,
Stan
-----Original Message-----
From: Robin Haw [mailto:[email protected]]
Sent: June-25-12 10:02 PM
To: Stanley Ng
Cc: [email protected]; Francis Ouellette; [email protected]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Hi Stan,
I'm glad I was able to forward the email to you. I think it should be
"referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".
Are you using the new utoronto email system? There's some odd behaviour with
the sending and receiving some emails with the utoronto mail system. So,
this might explain why you did not receive the email earlier because it was
definitely sent by our mail server and received at a number of different
locations.
If you have any other questions, please let me know.
Robin
________________________________________
From: Stanley Ng [[email protected]]
Sent: 25 June 2012 18:23
To: Robin Haw
Cc: [email protected]; Francis Ouellette; [email protected]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Hi Robin,
Thanks for your email.
I didn't receive the below email from David Croft for some reason. (nothing
in my inbox or junkmail folders)
I have written some small R scripts to help me collect entrez gene IDs for
each specified pathway.
Do you know what is the new attribute name I should be using to get lists of
NCBI gene IDs for pathways through the Biomart R module?
i.e., right now i am querying for "referencedatabase_entrez_gene" but it
doesn't work anymore, maybe it is called something else now?
Commands:
library("biomaRt")
mart = useMart("REACTOME", dataset="pathway") pathwayids =
getBM(attributes=c("stableidentifier_identifier"),filters="species_selection
",values=c("Homo sapiens"), mart=mart) pathwayids =
c(do.call("cbind",pathwayids)) entrezids =
getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list
",values=c(pathwayids[1]), mart=mart)
Error:
Query ERROR: caught BioMart::Exception::Usage: Attribute
referencedatabase_entrez_gene NOT FOUND</pre>
Thanks,
Stan
________________________________________
From: Robin Haw [[email protected]]
Sent: June 25, 2012 5:51 PM
To: Stanley Ng
Cc: [email protected]; Francis Ouellette; [email protected]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Dear Stanley,
Is this still a problem? I thought we'd been able to address this issue,
last week?
If not, can you please let us know?
Thanks,
Robin
________________________________________
From: [email protected]
[[email protected]] on behalf of David Croft
[[email protected]]
Sent: 22 June 2012 10:42
To: [email protected]
Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer
working?
Hi Stanley,
Sorry about this problem, we got caught out by a database name change:
Entrez gene is now NCBI gene. We have now updated our BioMart to reflect
this, so if you run the query on our website, it should work. I do not have
any experience with R-BioMart, you may need to experiment a little.
Cheers,
David Croft.
> I am a PhD student working on leukemia at the university of toronto.
>
> About a month ago, I ran the following query which returned a list of
entrez gene ids for the pathways that I was interested in.
>
> "library("biomaRt");
>
> mart = useMart("REACTOME", dataset="pathway")
>
> pathwayids =
> getBM(attributes=c("stableidentifier_identifier"),filters="species_sel
> ection",values=c("Homo sapiens"), mart=mart)
>
> entrezids =
getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list
",values=c(pathwayids[i]), mart=mart)"
>
> However I tried to run that same query today through R biomart and it no
longer works. I see the following error and was wondering if the query
requirements have changed for what I am seeking?
>
> "
> Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters =
"pathway_id_list", :
> Query ERROR: caught BioMart::Exception::Query: Query error occurred at
web service based data source!
>
> Remote data source: http://www.reactome.org:5555/biomart/martservice?
>
> Query XML:
> <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200"
count = "" softwareVersion = "0.6" requestId= "biomart-client">
> <Dataset name = "pathway" interface = "default" >
> <Attribute name =
"referencedatabase_entrez_gene" />
> <ValueFilter name = "pathway_id_list" value =
"REACT_1698"/>
> </Dataset>
> </Query>
>
> Please ensure the above query XML is well-formed and does not contain
illegal characters.
>
> Error message from remote server as below:
> Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Unknown column
'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entr
ez_gene' in 'field list'
>
> "
> _______________________________________________
> Reactome-help mailing list
> [email protected]
> https://lists.reactome.org/mailman/listinfo/reactome-help
_______________________________________________
Reactome-help mailing list
[email protected]
https://lists.reactome.org/mailman/listinfo/reactome-help
________________________________________
From: Stanley Ng [[email protected]]
Sent: 25 June 2012 16:50
To: Robin Haw
Cc: [email protected]; Francis Ouellette; [email protected]
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Hi Robin,
When do you think this can be fixed?
Thanks,
Stan
________________________________________
From: Stanley Ng
Sent: June 25, 2012 3:41 PM
To: [email protected]
Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected])
Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Hi Arek,
Thanks for clarifying. I had thought it may have been a new issue.
Stan
________________________________________
From: arek kasprzyk [[email protected]]
Sent: June 25, 2012 2:01 PM
To: Stanley Ng
Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected])
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
Hi Stan
This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l
will be able to help you
Sent from my BlackBerryR smartphone on O2
-----Original Message-----
From: Stanley Wai-Kwong Ng <[email protected]>
Sender: [email protected]
Date: Mon, 25 Jun 2012 13:35:19
To: 'Arek Kasprzyk'<[email protected]>
Cc: <[email protected]>
Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
