Hi, I have an affymetrix experiment with the following target file: Replicates FileName Target 8 SA100Hu133plus.CEL LR 4 SA101Hu133plus.CEL LR 4 SA102Hu133plus.CEL LR 4 SA103Hu133plus.CEL LR 9 SA104Hu133plus.CEL LR 5 SA105Hu133plus.CEL LR 5 SA106Hu133plus.CEL LR 10 SA107Hu133plus.CEL LR 11 SA108Hu133plus.CEL LR 12 SA109Hu133plus.CEL MET 13 SA111Hu133plus.CEL MET 14 SA112Hu133plus.CEL MET 15 SA113Hu133plus.CEL MET 16 SA114Hu133plus.CEL MET 17 SA115Hu133plus.CEL MET 18 SA116Hu133plus.CEL MET 6 SA117Hu133plus.CEL MET 6 SA119Hu133plus.CEL MET 19 SA121Hu133plus.CEL METD 20 SA122Hu133plus.CEL METD 7 SA123Hu133plus.CEL METD 7 SA124Hu133plus.CEL METD 21 SA127Hu133plus.CEL HR 1 SA83Hu133plus.CEL HR 1 SA84Hu133plus.CEL HR 1 SA85Hu133plus.CEL HR 22 SA86Hu133plus.CEL HR 2 SA87Hu133plus.CEL HR 2 SA88Hu133plus.CEL HR 2 SA89Hu133plus.CEL HR 23 SA90Hu133plus.CEL HR 3 SA92Hu133plus.CEL HR 3 SA93Hu133plus.CEL HR 24 SA94Hu133plus.CEL HR 25 SA95Hu133plus.CEL HR 26 SA96Hu133plus.CEL HR 27 SA98Hu133plus.CEL LR 28 SA99Hu133plus.CEL LR where files with the same number under replicates column are blocks of the technical replicates of the sames biological replicate. and the following design: LR HR MET METD SA100Hu133plus.CEL 1 0 0 0 SA101Hu133plus.CEL 1 0 0 0 SA102Hu133plus.CEL 1 0 0 0 SA103Hu133plus.CEL 1 0 0 0 SA104Hu133plus.CEL 1 0 0 0 SA105Hu133plus.CEL 1 0 0 0 SA106Hu133plus.CEL 1 0 0 0 SA107Hu133plus.CEL 1 0 0 0 SA108Hu133plus.CEL 1 0 0 0 SA109Hu133plus.CEL 0 0 1 0 SA111Hu133plus.CEL 0 0 1 0 SA112Hu133plus.CEL 0 0 1 0 SA113Hu133plus.CEL 0 0 1 0 SA114Hu133plus.CEL 0 0 1 0 SA115Hu133plus.CEL 0 0 1 0 SA116Hu133plus.CEL 0 0 1 0 SA117Hu133plus.CEL 0 0 1 0 SA119Hu133plus.CEL 0 0 1 0 SA121Hu133plus.CEL 0 0 0 1 SA122Hu133plus.CEL 0 0 0 1 SA123Hu133plus.CEL 0 0 0 1 SA124Hu133plus.CEL 0 0 0 1 SA127Hu133plus.CEL 0 1 0 0 SA83Hu133plus.CEL 0 1 0 0 SA84Hu133plus.CEL 0 1 0 0 SA85Hu133plus.CEL 0 1 0 0 SA86Hu133plus.CEL 0 1 0 0 SA87Hu133plus.CEL 0 1 0 0 SA88Hu133plus.CEL 0 1 0 0 SA89Hu133plus.CEL 0 1 0 0 SA90Hu133plus.CEL 0 1 0 0 SA92Hu133plus.CEL 0 1 0 0 SA93Hu133plus.CEL 0 1 0 0 SA94Hu133plus.CEL 0 1 0 0 SA95Hu133plus.CEL 0 1 0 0 SA96Hu133plus.CEL 0 1 0 0 SA98Hu133plus.CEL 1 0 0 0 SA99Hu133plus.CEL 1 0 0 0 My question is should I run duplicateCorrelation function with this vector B<-c( 8, 4, 4, 4, 9, 5, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 6, 6, 19, 20, 7, 7, 21, 1, 11, 22, 2, 2, 2, 23, 3, 3, 24, 25, 26, 27, 28) where each biological replicate gets different block number or B<-c( 4, 4, 4, 5, 5, 6, 6, 7, 7, 2, 2, 2, 3, 3, ) where I ignore biological replicates or maybe put zero instead of biological replicates. corfit <- duplicateCorrelation(data, design, block=B) Thanks Ron

> Date: Mon, 09 May 2005 16:34:02 +0300 > From: "Ron Ophir" <ron.ophir@weizmann.ac.il> > Subject: [BioC] LIMMA: Unbalanced technical replicates > To: <bioconductor@stat.math.ethz.ch> > > Hi, > I have an affymetrix experiment with the following target file: > Replicates FileName Target > 8 SA100Hu133plus.CEL LR > 4 SA101Hu133plus.CEL LR > 4 SA102Hu133plus.CEL LR > 4 SA103Hu133plus.CEL LR > 9 SA104Hu133plus.CEL LR > 5 SA105Hu133plus.CEL LR > 5 SA106Hu133plus.CEL LR > 10 SA107Hu133plus.CEL LR > 11 SA108Hu133plus.CEL LR > 12 SA109Hu133plus.CEL MET > 13 SA111Hu133plus.CEL MET > 14 SA112Hu133plus.CEL MET > 15 SA113Hu133plus.CEL MET > 16 SA114Hu133plus.CEL MET > 17 SA115Hu133plus.CEL MET > 18 SA116Hu133plus.CEL MET > 6 SA117Hu133plus.CEL MET > 6 SA119Hu133plus.CEL MET > 19 SA121Hu133plus.CEL METD > 20 SA122Hu133plus.CEL METD > 7 SA123Hu133plus.CEL METD > 7 SA124Hu133plus.CEL METD > 21 SA127Hu133plus.CEL HR > 1 SA83Hu133plus.CEL HR > 1 SA84Hu133plus.CEL HR > 1 SA85Hu133plus.CEL HR > 22 SA86Hu133plus.CEL HR > 2 SA87Hu133plus.CEL HR > 2 SA88Hu133plus.CEL HR > 2 SA89Hu133plus.CEL HR > 23 SA90Hu133plus.CEL HR > 3 SA92Hu133plus.CEL HR > 3 SA93Hu133plus.CEL HR > 24 SA94Hu133plus.CEL HR > 25 SA95Hu133plus.CEL HR > 26 SA96Hu133plus.CEL HR > 27 SA98Hu133plus.CEL LR > 28 SA99Hu133plus.CEL LR > where files with the same number under replicates column are blocks of > the technical replicates of the sames biological replicate. > and the following design: > LR HR MET METD > SA100Hu133plus.CEL 1 0 0 0 > SA101Hu133plus.CEL 1 0 0 0 > SA102Hu133plus.CEL 1 0 0 0 > SA103Hu133plus.CEL 1 0 0 0 > SA104Hu133plus.CEL 1 0 0 0 > SA105Hu133plus.CEL 1 0 0 0 > SA106Hu133plus.CEL 1 0 0 0 > SA107Hu133plus.CEL 1 0 0 0 > SA108Hu133plus.CEL 1 0 0 0 > SA109Hu133plus.CEL 0 0 1 0 > SA111Hu133plus.CEL 0 0 1 0 > SA112Hu133plus.CEL 0 0 1 0 > SA113Hu133plus.CEL 0 0 1 0 > SA114Hu133plus.CEL 0 0 1 0 > SA115Hu133plus.CEL 0 0 1 0 > SA116Hu133plus.CEL 0 0 1 0 > SA117Hu133plus.CEL 0 0 1 0 > SA119Hu133plus.CEL 0 0 1 0 > SA121Hu133plus.CEL 0 0 0 1 > SA122Hu133plus.CEL 0 0 0 1 > SA123Hu133plus.CEL 0 0 0 1 > SA124Hu133plus.CEL 0 0 0 1 > SA127Hu133plus.CEL 0 1 0 0 > SA83Hu133plus.CEL 0 1 0 0 > SA84Hu133plus.CEL 0 1 0 0 > SA85Hu133plus.CEL 0 1 0 0 > SA86Hu133plus.CEL 0 1 0 0 > SA87Hu133plus.CEL 0 1 0 0 > SA88Hu133plus.CEL 0 1 0 0 > SA89Hu133plus.CEL 0 1 0 0 > SA90Hu133plus.CEL 0 1 0 0 > SA92Hu133plus.CEL 0 1 0 0 > SA93Hu133plus.CEL 0 1 0 0 > SA94Hu133plus.CEL 0 1 0 0 > SA95Hu133plus.CEL 0 1 0 0 > SA96Hu133plus.CEL 0 1 0 0 > SA98Hu133plus.CEL 1 0 0 0 > SA99Hu133plus.CEL 1 0 0 0 > My question is should I run duplicateCorrelation function with this > vector > B<-c( 8, 4, 4, 4, 9, 5, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, > 6, 6, 19, 20, 7, 7, 21, 1, 11, 22, 2, 2, 2, 23, 3, 3, 24, 25, > 26, 27, 28) > where each biological replicate gets different block number Yes. > or > B<-c( 4, 4, 4, 5, 5, 6, 6, 7, 7, 2, 2, 2, 3, 3, ) > where I ignore biological replicates or maybe put zero instead of > biological replicates. No. > corfit <- duplicateCorrelation(data, design, block=B) 'block=targets$Replicate' would be fine. Gordon > Thanks > Ron