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

cstrato cstrato at aon.at
Wed Aug 11 23:25:47 CEST 2010

Dear Stacy,

Since you mention xps, it may be of interest to you that xps supports 
four background algorithms:
- rma background
- sector background (mas4)
- weigthed sector background (mas5)
- gccontent background
(see vignette xpsPreprocess.pdf)

For the ST 1.0 arrays you can use gccontent background with the generic 
background probes by setting parameter "bgcorrect.select" either to 
"genomic" or "antigenomic".

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 8/11/10 4:51 PM, Stacy_Xu at bd.com wrote:
>     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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