How do I convert a list of agilent probe IDs to gene symbols using biomaRt and have na values?

Question

I'm trying to use biomaRt to convert a list of more than 90k probe IDs to the gene symbols, but am having problems. Using the getBM function, I can see that only 22k of those have corresponding gene symbols, but the output is a vector of length 22k, and I am unable to see the correspondence to the initial probe ID list. Using getBMlist, I can get an output with na values specified for those probes that don't match, but the function gives a warning message that getBMlist isn't for large lists. How do I get an output of 90k gene symbols and na values?

Answer 1

To get the mappings between probeID and gene symbol you need to include the probeID in the biomaRt attributes.

Here's how I did it for some of my work using agilent microarrays:

genes<-c("A_23_P10060", "A_23_P10091", "A_23_P103951", "A_23_P10525", "A_23_P105732", "A_23_P10605", "NM_005325")

library(biomaRt)
ensembl<-useMart("ensembl", dataset="hsapiens_gene_ensembl")

ensembl.id<-grep("ENST", genes, value=T)
agilent.df<-getBM(attributes = c("hgnc_symbol","efg_agilent_wholegenome_4x44k_v1"), filters=c("efg_agilent_wholegenome_4x44k_v1"),values=genes, mart=ensembl)

genes<-merge(x = as.data.frame(genes),y =  agilent.df, by.y="efg_agilent_wholegenome_4x44k_v1", all.x=T, by.x="genes")

There is a very good biomaRt tutorial that walks you though the same process. If you run this code you'll notice that one probe will have "" for a hgnc_symbol, that's because it exists in the ensemble mart but has no designated gene symbol.