Question: Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_name"), : could not find function "featureNames"
0
gravatar for pratikshasharma47
5 months ago by
pratikshasharma470 wrote:

Hi! I'm new to R and I'm trying to do GO enrichment analysis using biomaRT. I have affymetrix data of rice (GPL2025) I have run the following script:

> library(biomaRt)                                                                                                                                                                             
> mart <- useEnsembl("plants_mart", "osativa_eg_gene",host = "plants.ensembl.org")                                                              
> annot <- getBM(c("affy_rice","ensembl_gene_id","entrezgene","external_gene_name"), "affy_rice",featureNames(z), mart)
Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_name"),  : 
  could not find function "featureNames"

any information to get rid of this error.

ADD COMMENTlink modified 5 months ago by Mike Smith3.9k • written 5 months ago by pratikshasharma470
Answer: Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_na
1
gravatar for Mike Smith
5 months ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

You'll need to load the package where featureNames() is defined. This is in Biobase rather than biomaRt, so you should add the line library(Biobase) to the top of your script.

If you see an error like this in the future you can search the help files for all the package you have installed using ?? e.g. ??featureNames. This will hopefully help you find the package where a function is defined.

ADD COMMENTlink written 5 months ago by Mike Smith3.9k
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