Unable to use biomaRt package to get Gene Symbols from Entrez IDs

问题

I am using the following code to retrieve Gene Symbols from Entrez IDs:

library("biomaRt")
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org")

g <- getBM(c("hgnc_symbol"), filters = "entrezgene", c(entrez), ensembl)

but I get the following error:

Error in value[[3L]](cond): Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.
Traceback:

1. getBM(c("hgnc_symbol"), filters = "entrezgene", c(entrez), ensembl)
2. tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery), 
 .     error = function(e) {
 .         stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")
 .     })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")

回答1:

library(biomaRt)
marts <- listMarts()
ensembl <- useMart("ensembl")
datasets <- listDatasets(ensembl)
ensembl=useDataset("hsapiens_gene_ensembl",mart=ensembl)
attributes <- listAttributes(ensembl)
my_ids <- read.csv("/home/firat/Desktop/ahmet_deseq2_results.csv")
results_end_1 <- getBM(attributes = c("ensembl_gene_id","external_gene_name"), values = my_ids, mart = ensembl )
View(results_end_1)
merged_with_my_ids <- merge(my_ids,results_end_1,by.x = "X",by.y = ,"ensembl_gene_id")
View(merged_with_my_ids)

Here is how I use biomaRt. I think it is self explanatory. The lines until my_ids are quiet the same for every script. For your case, in attributes = "entrezgene" would be useful instead of me using "ensembl_gene_id". Merging is an important step. In my case, while merging, by.x= "X" means, in my_ids csv, the ensemblegeneid's were located in a column named "X". so what I am basicly saying is, from my_ids, match the X column with results_end_1's "ensembl_gene_id" column and merge. If anything that is not clear, please ask. Fırat