I want to add gene name information to my expression file, I use Biomart for this, but actually I did not get any result from getBM,
My code in R:
upregul<-read.csv(file.choose()) View(upregul) library(biomaRt) listEnsembl() ensembl <- useEnsembl(biomart = "genes") ensembl_ids<-(upregul) View(ensembl_ids) datasets <- listDatasets(ensembl) head(datasets) ensembl_con<-useEnsembl("ensembl",dataset="hsapiens_gene_ensembl") attr<-listAttributes(ensembl_con) filters<-listFilters(ensembl_con) theBm<-getBM(attributes = c("ensembl_gene_id","external_gene_name"), filters = "ensembl_gene_id", values = ensembl_ids$X , mart =ensembl_con)
The result after running the getBM:
 ensembl_gene_id external_gene_name <0 rows> (or 0-length row.names)
Can you update your post to show some examples of what's in your
ensembl_idsobject? Perhaps the contents of
It's hard to say why this might be happening without seeing at least a small example of the data you are using.
Exclude commands you use to examine the data (such as
head()or just typing in the object name which prints a representation of the object to the Console) when you share your code here.
Many thanks, it worked. but at first, I had 5000 observations and after getBM, my obs reduced to 4000.