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

On Wed, Oct 7, 2009 at 11:02 AM, Michael Black <mblack@virginia.edu> wrote: > 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. > > Check the list archives (see bottom of the message for a link). There have been several discussions on this topic in the last couple of months. Sean [[alternative HTML version deleted]]