[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.
Thanks,
Stacy
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