[Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

[Christos Hatzis]

Hello,

For many genes, as in the example below, there are more than one Affy probe
sets that interrogate the same transcript.  Is there a way to rank those
probe sets relative to their proximity to the 3' end of the gene?  I wasn't
sure whether there are annotation packages that provide the genomic
coordinates of the probes in a probe set.

> testids <- c("206527_at","209459_s_at","209460_at")
> library(biomaRt)
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> probAttrs <- c("affy_hg_u133a", "hgnc_symbol", "chromosome_name", 
 	"start_position", "end_position", "strand") 
> testres <- getBM(attributes = probAttrs, filters = "affy_hg_u133a", values
= 
	testids, mart = ensembl) 
> testres
  affy_hg_u133a hgnc_symbol chromosome_name start_position end_position
strand
1   209459_s_at        ABAT              16        8768422      8878432
1
2     209460_at        ABAT              16        8768422      8878432
1
3     206527_at        ABAT              16        8768422      8878432
1

Thank you.   
-Christos

Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park, Suite 5350
Woburn, MA 01801