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

[Stacy_Xu at bd.com]

   Thanks James, that's exactly what we are looking for.

   From:    "James W. MacDonald" <jmacdon at med.umich.edu>
   To:      Stacy_Xu at bd.com
   Cc:      bioconductor at stat.math.ethz.ch
   Date:    08/12/2010 02:33 AM
   Subject: Re: [BioC] Affy ST 1.0 gene chip background probes cut off set up
     _________________________________________________________________

   Hi Stacy,
   On 8/11/2010 10:51 AM, 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.
   Actually, I believe those are what you want (and I count 45 of them).
   Note that Affy states there are 17k _probes_, not probesets. If you look
   at the number of probes in a probeset for controls, you will see that
   they can number in the thousands. For instance, the AFFX-Bs-thr_st
   control probeset has 1189 probes.
   And the data for these controls are in the celfile, as they are used by
   Affy's software. However, the cdf package that we make available for
   this chip, which is based on the unsupported cdf from Affy, doesn't
   contain the locations for these probesets.
   However, the pd.hugene.1.1.st.v1 package that you can use in conjunction
   with the oligo package does contain these probe locations. As a check, I
   downloaded the annotation csv file from Affy and grep'ed out the
   antigenomic probe IDs. I then loaded up the pd.hugene.1.1.st.v1 package
   and looked to see how many probes there are:
   > bgp <- read.csv("bgp.csv", header=F) ## csv file with only
   antigenomic probes
   > dim(bgp)
   [1] 45 39
   > sql <- paste("select * from pmfeature where fsetid in ('",
   paste(bgp[,1], collapse = "','"), "');", sep = "")
   > library(pd.hugene.1.1.st.v1)
   > con <- db(pd.hugene.1.1.st.v1)
   > a <- dbGetQuery(con, sql)
   > nrow(a)
   [1] 16943
   So the 45 antigenomic probesets have just about 17k probes.
   AFAIK, oligo uses basic RMA to do background correction, so would not
   use these antigenomic probes. However, you can access them if you are
   willing to do some work.
   Best,
   Jim
   >     Thanks,
   >     Stacy
   >
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   --
   James W. MacDonald, M.S.
   Biostatistician
   Douglas Lab
   University of Michigan
   Department of Human Genetics
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