Dear Sir/Madam, The bioinformaticist whom we cooperated with analyzed the Agilent microarray data with LIMMA and Genespring. As what she said, LIMMA should be more stringent than Genespring, so that we can get more genes with Genespring analysis, but in fact we get less genes by Genespring sometimes and sometimes ¼ of the genes are different, even we both use ANOVA and Benjamini & Hochberg for statistic analysis. So my question is: 1 Is this kind of situation reasonable? 2 What' the reason for the different results between LIMMA and Genespring? Best wihses! Ming ________________________________ Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671 [[alternative HTML version deleted]]

Hello Ming, Hard to say something about your data without details on your preprocessing. The biggest difference in my experience is from the background subtraction and normalization steps. Check the normalization section of Agilent Feature Extraction software. This is what gives the green and red processed values. We use Arabidopsis 4x44k slides. Personally, I do not use the Agilent processed values. The log-fold changes fishtail at low expression levels. That is why I see the differences there. I start with g(and r)MeanSignal and g(and r)BGMedianSignal, and use limma to do the background subtraction and normalization steps. Edwin -- On Mon, 12 Dec 2011 14:42:38 +0100 "Jin, Ming" <ming.jin at="" helmholtz-muenchen.de=""> wrote: > Dear Sir/Madam, > > The bioinformaticist whom we cooperated with analyzed the Agilent > microarray data with LIMMA and Genespring. As what she said, LIMMA > should be more stringent than Genespring, so that we can get more > genes with Genespring analysis, but in fact we get less genes by > Genespring sometimes and sometimes ? of the genes are different, even > we both use ANOVA and Benjamini & Hochberg for statistic analysis. So > my question is: > 1 Is this kind of situation reasonable? > 2 What' the reason for the different results between LIMMA and > Genespring? > > Best wihses! > > Ming > > ________________________________ > Helmholtz Zentrum M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 > > [[alternative HTML version deleted]] > Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032948