Dear Sergio, The duplicateCorrelation document tells you that you need 2 more arrays than coefficients defined by the design matrix, and I think that you have already read that. You are, in effect, asking whether the documentation is correct. It is. Getting a correlation of 1 is exactly the sort of thing which will happen if you don't have the minimum number of arrays. Best wishes Gordon > Date: Wed, 21 Feb 2007 10:31:16 -0800 > From: Sergio Barberan <barberan at="" biology.ucsc.edu=""> > Subject: [BioC] duplicateCorrelation with few arrays > To: bioconductor at stat.math.ethz.ch > Message-ID: <1172082676.10408.234.camel at elegans.ucsc.edu> > Content-Type: text/plain > > Hi, > > It is possible that my only problem is that I'm trying to use > duplicateCorrelation with few arrays but I just wanted to be sure. > > My slides include three replicas of each spot 120 spots apart; > to make sure I'm giving duplicateCorrelation the right input I do: > > unwrapdups(MA$genes$Name, ndups=3, spacing=120) > > and I do obtain a matrix with identical columns with the replica spots > on it. > > My problem is that when I try to calculate: > > cor <- duplicateCorrelation(MA,design,ndups=3,spacing=120) > > I get several warnings: 1: NaNs produced in: sqrt(dfitted.values) > > and I get a correlation of 1. > > Right now I do not have two more arrays than the column rank of design, > but I was still trying to get some results; is this the problem or is > there something I'm doing wrong. > > Thanks in advance for your help, > Sergio