biomaRt - rice genes database not working
1
0
Entering edit mode
XUEPING • 0
@fc25ea0d
Last seen 2.8 years ago
Japan

Hello!

I'm having a problem with the rice genes database.

I'm using Package biomaRt version 2.40.5

the R version is R 3.6.1

library(biomaRt)

ensembl = useMart(biomart = "plants_mart",host = "http://plants.ensembl.org",dataset="osativa_eg_gene")

a <- read.csv(file = "43id.csv",header = F)

b<-a[,1]

supplement <- getBM(attributes =c("ensembl_gene_id",'ensembl_transcript_id',"description"),filters = "ensembl_gene_id",values =b,mart = ensembl)

And when I use:

supplement <- getBM(attributes =c("ensembl_gene_id",'ensembl_transcript_id',"description"),filters = "ensembl_gene_id",values =b,mart = ensembl)

I get the error like this

supplement <- getBM(attributes =c("ensembl_gene_id",'ensembl_transcript_id',"description"),filters = "ensembl_gene_id",values =b,mart = ensembl) Error in getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id", : Query ERROR: caught BioMart::Exception::Database: Error during query execution: Illegal mix of collations for operation ' IN '

Thanks for the help

Kind regards,

Jayia

biomaRt • 672 views
ADD COMMENT
0
Entering edit mode
swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 3 hours ago
San Diego

Ensembl does occasionally go down and stop working for everyone, but I'm not sure that's what you've got.

Since the problem is probably with your b list of values, it would help if you provided what head(b) is. If its a dataframe, and not a vector, that's a problem.

ADD COMMENT

Login before adding your answer.

Traffic: 534 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6