While doing the gene mapping from Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for a sample. My work revolves around gene names only. Please suggest the appropriate step to deal with this situation. The code is as follows:
require("biomaRt")
mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useDataset("hsapiens_gene_ensembl", mart)
annotLookup <- getBM(
mart=mart,
attributes=c(
"affy_hg_u133_plus_2",
"ensembl_gene_id",
"gene_biotype",
"external_gene_name"),
filter = "affy_hg_u133_plus_2",
values = rownames(exprs(gset))[1:dim(exprs(gset))[1]], uniqueRows=TRUE)
A sample output snap is attached for reference.
Thank you.