Dear List Members, in limma manual is stated that "A zero weight indicates that the spot should be ignored in all analysis as being unreliable". lmFit function uses information from weights. Is that means that zero-weight spots will not be used in functions: contrasts.fit, eBayes, decideTests and topTable? I.e. is zero-weight spot treated as having missing values for fluorescence in these functions? Best Regards, Maciej Jończyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1

Yes, the limma manual means what it says. Best wishes Gordon > Date: Tue, 23 Aug 2011 17:17:44 GMT > From: mjonczyk at biol.uw.edu.pl > To: bioconductor at r-project.org > Subject: [BioC] [limma] 0 weights = removed from analysis? > Message-ID: <201108231717.p7NHHf0g003682 at woreczko.biol.uw.edu.pl> > > Dear List Members, > > in limma manual is stated that > "A zero weight indicates that the spot should be ignored in all analysis as > being unreliable". > lmFit function uses information from weights. > Is that means that zero-weight spots will not be used in functions: > contrasts.fit, eBayes, decideTests and topTable? I.e. is zero-weight spot > treated as having missing values for fluorescence in these functions? > > Best Regards, > Maciej Jończyk, MSc > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa > 1 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}