[BioC] Affy ST 1.0 gene chip background probes cut off set up

Stacy_Xu at bd.com Stacy_Xu at bd.com
Wed Aug 11 16:51:38 CEST 2010

   Hi, guys
   There are several ways to do the background corrections for the new ST 1.0
   chip from Affy from bio-conductor like xps, affy-aroma,pdfInfo and rma. And
   almost all of those have a parameter to indicate background correction or
   subtraction.  According  to  Affy  data  sheet for human ST 1.0 array,
   "Background  is  estimated using a set of approximately 17,000 generic
   background probes. Standard poly-A controls and hybridization controls are
   represented on the arrays to allow convenient troubleshooting along the
   entire experimental process."
   I am wondering are the information or IDs of those 17,000 background RNA
   probes somewhere in the CEL file where I can set up my negative cut off
   expression level? They do have some "antigenomic" controls, but there are
   only about 60 of those and they are not what we want.
   This message (which includes any attachments) is intended only for the
   designated  recipient(s).  It  may contain confidential or proprietary
   information and may be subject to the attorney-client privilege or other
   confidentiality protections. If you are not a designated recipient, you may
   not review, use, copy or distribute this message. If you receive this in
   error, please notify the sender by reply e-mail and delete this message.
   Thank you.

More information about the Bioconductor mailing list