We have evaluated the methods in Lumi using the MAQC benchmark data. The publication is under review. Pan, can you add the inter-lab concordance comparison results (Three curves: raw, Beadstudio, and lumi) in the lumi manual? Thanks! Simon ================ Date: Tue, 19 Jun 2007 11:42:43 +0200 From: "daneel jordan" <daneel.robert@gmail.com> Subject: [BioC] Illumina Treatment To: bioconductor at stat.math.ethz.ch Message-ID: <e88c6fe60706190242y1a0e8a22l7d91cddd854344a9 at="" mail.gmail.com=""> Content-Type: text/plain Dear Bioconductor user, I need general help in illumina data treatments. I previously see that there is Lumi packages to treat data, but I didn't see any benchmarch to compare data normalization provided by lumi, and the ones from BeadStudio. (if you have any can you provide any link?); with no benchmarks I would like to keep the analysis as much standart as possible, using Rank-invariant from Bead Studio. Unfortunately, as you may know for sure, this treatment create negative values, because of bg subtraction, after log transformation, I have NaN value, when I run a simple ttest analysis for each line of the array it can happen that it complains for NAN values. what do you suggest? add to the all chip a minim value in order to eliminate all possible negative values? threshold the data for negative values? is there any way to tell the function t.test to not consider NaN fields? Daneel [[alternative HTML version deleted]]