Dear Ming, Limma borrows information between genes, whereas Genespring does not. This gives limma more statistical power to detect more differentially expressed genes, and also produces as more reliable gene ranking with fewer false discoveries. When the sample sizes are small, the differences can be dramatic. See Shirley Liu's primer published in Nature Genetics for a tutorial on what limma does and why it works: http://www.nature.com/nbt/journal/v28/n4/abs/nbt.1619.html For reasons that I don't understand, Genespring has chosen not to implement any of the statistical methods developed in the past decade or so for differential expression of microarrays. They stick to t-tests and anova methods from early last century, methods that are unsuitable for genomic data with small samples sizes. As has been remarked by another poster, there may be other differences as well between Genespring as limma as to do with pre-processing. Best wishes Gordon > Date: Mon, 12 Dec 2011 14:42:38 +0100 > From: "Jin, Ming" <ming.jin at="" helmholtz-muenchen.de=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] Difference between LIMMA and Genespring > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}