library(biomaRt)
mart.hs <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
# get probeset IDs for transcript cluster 2315633
huex <- read.table("~/Downloads/HuEx-1_0-st-v2.na32.hg19.probeset.csv", sep = ",", stringsAsFactors = F, header = T)
probes <- subset(huex, transcript_cluster_id == "2315633")$probeset_id
# get gene symbols
genes <- getBM(attributes = c("affy_huex_1_0_st_v2", "hgnc_symbol"), filters = "affy_huex_1_0_st_v2", values = probes, mart = mart.hs)
genes
# affy_huex_1_0_st_v2 hgnc_symbol
#1 2315638 B3GALT6
#2 2315642 B3GALT6
#3 2315639 B3GALT6
#4 2315643 B3GALT6
#5 2315644 B3GALT6
#6 2315640 B3GALT6
#7 2315637 B3GALT6
#8 2315645 B3GALT6
#9 2315641 B3GALT6
Friday, April 11, 2014
Mapping between Affymetrix exon array Features to Genes
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