Hi, could you please explain what the difference is between "the local background subtraction" and the global background subtraction as done by BeadStudio normalization? Thanks very much! Jin ------------------------------ Message: 4 Date: Fri, 22 Jun 2007 10:36:10 -0400 From: "Peter" <pwilkinson_m@hotmail.com> Subject: Re: [BioC] Illumina Treatment To: "'daneel jordan'" <daneel.robert at="" gmail.com=""> Cc: bioconductor at stat.math.ethz.ch Message-ID: <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. Peter ______________________________________________________________________ ______________ TV dinner still cooling?