[BioC] Searching miRNA probe ids and annotating probe id lists
Michael Black
mblack at virginia.edu
Wed Oct 7 17:02:26 CEST 2009
Hopefully a simple question. A user ran a very simple experiment of a
pair of Affy miRNA array (first miRNA run for our core facility).
I've made a quick and dirty BioC cdf from the Affy cdf and ran the
pair of chips through RankProd to pull out a list of up/down regulated
probe ids. But miRBase has no facility to batch search those probe
ids, and neither does Affy's web site. Am I just being dense and
missing something, or is there a simple way to match Affy miRNA probe
ids to miRBase accessions? Or should I just be parsing out the
genomic coordinate information from the Affy CSV annotations directly
anyway?
This is my first ever exposure to miRNA array data, so any direction
on how to go from probe id's to annotated genomic data as simply as
possible would be appreciated.
_________________________________
Michael B. Black, Ph.D.
Bioinformatics Computing Support
University of Virginia
ITC-Academic Computing Health Sciences
mblack at virginia.edu
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