[BioC] illumina treatment

Jin Peng ae4899jin at yahoo.com
Sun Jun 24 00:40:44 CEST 2007

Hi, could you please explain what the difference is

"the local background subtraction" 


 the global background subtraction as done by
BeadStudio normalization?

Thanks very much!



Message: 4
Date: Fri, 22 Jun 2007 10:36:10 -0400
From: "Peter" <pwilkinson_m at hotmail.com>
Subject: Re: [BioC] Illumina Treatment
To: "'daneel jordan'" <daneel.robert at gmail.com>
Cc: bioconductor at stat.math.ethz.ch
<002301c7b4da$b1d142a0$7700000a at wilkz60mi2>
Content-Type: text/plain;	charset="us-ascii"

This is in fact what we do here in Montreal. We find
that the beadstudio
software is kind of useless. Using version 3.x, we
export the raw
probe-level data, and surrogate replace all any values
that are below the
background controls  using next largest log value
+1;ex if the mean
background controls are 59 we replace with 64+1 or 65
(2^n+1), if its 110 it
would be 128+1 or 129. This eliminates the issue of
negative numbers.
Background subtraction just makes the analysis more
difficult (especially
doing local background subtraction on some platforms)

Then we perform  the quantile normalization using the
functions in Limma.


TV dinner still cooling?

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