Dear Karen, The design matrix certainly does affect the duplicateCorrelations(), so I suspect that you've made a bookkeeping error. Either that or your data is artificial and has a some symmetry built into it. Best wishes Gordon >Date: Fri, 1 Dec 2006 16:09:16 -0800 >From: "Karen Vranizan" <vranizan at="" berkeley.edu=""> >Subject: [BioC] limma duplicateCorrelation question >To: <bioconductor at="" stat.math.ethz.ch=""> >Content-Type: text/plain > >The following two commands give me the same result for corfit$consensus: > >corfit<-duplicateCorrelation(MA,c(1,1,1,1,1,1),ndups=1,block=(1,1,2,2 ,3,3)) > >corfit<-duplicateCorrelation(MA,c(1,-1,1,-1,1,-1),ndups=1,block=(1,1, 2,2,3,3)) > >It seems that the design vector argument doesn't affect the >calculations. Is that correct? If not, then why is the design >vector used here? > >Thank you. > >Karen Vranizan >Functional Genomics Lab >261A Life Sciences Addition >Mail Code #3200 >UC Berkeley, CA 94720-3200 > >Phone: 510-642-7520 >Fax: 510-643-2685 >email: vranizan at berkeley.edu