Question: Problem using biomaRt with local database
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12.8 years ago by
Alessandro Bruselles100 wrote:
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ADD COMMENTlink modified 12.8 years ago • written 12.8 years ago by Alessandro Bruselles100
Answer: Problem using biomaRt with local database
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gravatar for Alessandro Bruselles
12.8 years ago by
Alessandro Bruselles100 wrote:
> Alessandro Bruselles <a.bruselles at="" ...=""> writes: Hi, I'm having some problems when trying to use biomaRt with a local install database; I've downloaded and installed locally the ensembl biomart database version ensembl_mart_42, (ftp://ftp.ensembl.org/pub/release-42/mart_42/data/mysql/ensembl_mart _42) I created all the tables and populated them... I get the following error when trying to connect to it with useMart: > library(biomaRt) Carico il pacchetto richiesto: XML Carico il pacchetto richiesto: RCurl > ensembl=useMart("ensembl_mart_42", dataset="hsapiens_gene_ensembl", host="pendragon.bio.uniroma2.it", user="brusel", password="*******", local = TRUE, mysql = TRUE) Carico il pacchetto richiesto: RMySQL Carico il pacchetto richiesto: DBI Errore in `dimnames<-.data.frame`(`*tmp*`, value = list(character(0), c("name", : 'dimnames' fornita per i ldata frame non valida I'm using R 2.4.0 and biomaRt 1.8.1 Any help will be very very appreciated Thanks. For any of you having the same problem, I solved the problem using the developmental version (1.9.14). __________________________ Alessandro Bruselles
ADD COMMENTlink written 12.8 years ago by Alessandro Bruselles100
Answer: Problem using biomaRt with local database
0
gravatar for Alessandro Bruselles
12.8 years ago by
Alessandro Bruselles100 wrote:
> Alessandro Bruselles <a.bruselles at="" ...=""> writes: Hi, I'm having some problems when trying to use biomaRt with a local install database; I've downloaded and installed locally the ensembl biomart database version ensembl_mart_42, (ftp://ftp.ensembl.org/pub/release-42/mart_42/data/mysql/ensembl_mart _42) I created all the tables and populated them... I get the following error when trying to connect to it with useMart: > library(biomaRt) Carico il pacchetto richiesto: XML Carico il pacchetto richiesto: RCurl > ensembl=useMart("ensembl_mart_42", dataset="hsapiens_gene_ensembl", host="pendragon.bio.uniroma2.it", user="brusel", password="*******", local = TRUE, mysql = TRUE) Carico il pacchetto richiesto: RMySQL Carico il pacchetto richiesto: DBI Errore in `dimnames<-.data.frame`(`*tmp*`, value = list(character(0), c("name", : 'dimnames' fornita per i ldata frame non valida I'm using R 2.4.0 and biomaRt 1.8.1 Any help will be very very appreciated Thanks. For any of you having the same problem, I solved the problem using the developmental version (1.9.14). __________________________ Alessandro Bruselles
ADD COMMENTlink written 12.8 years ago by Alessandro Bruselles100
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