biomaRt - rice genes database not working
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XUEPING • 0
@fc25ea0d
Last seen 3 months 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 • 131 views
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Entering edit mode
swbarnes2 ▴ 850
@swbarnes2-14086
Last seen 1 hour 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.

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