Dear Bioconductor, I am working with a loop design with both biological and technical replication, and am having difficulty incorporating both types of replication appropriately. I am looking at the both strain and the treatment level effects, will make most all possible contrasts, and would like to test this over the biorep error. My experiment follows, with 6 different strain/treatments (CD,CW,HD,HW,VD,VW), 3 bio reps per strain/treat (1,2,3) and 2 techreps per biorep. Slide Cy3 Cy5 1 VW3 HW2 2 HW2 HD1 3 HD2 HW1 4 VD3 HD2 5 CD1 HD3 6 CW1 HW3 7 VW2 VD1 8 VD2 VW1 9 CD3 VD2 10 CW3 VW2 11 HW1 VW3 12 HD3 VD3 13 CW2 CD1 14 HD1 CD2 15 CD2 CW1 16 VW1 CW2 17 VD1 CD3 18 HW3 CW3 It seems like I could use single-channel analysis, and use duplicate correlation to indicate which file and channels are the technical reps. I am getting an error when attempting to do this targets2 <- targetsA2C(targets) u <- unique(targets2$Target) f <- factor(targets2$Target, levels=u) design <- model.matrix(~0+f) colnames(design) <- u biolrep <-c(11,18,7,11,10,8,8,15,9,1,12,4,13,17,16,14,14,3,17,6,18,10,15,9,1,5 ,2,7,4,2,5,16,3,13,6,12) corfit <-duplicateCorrelation(MAAq, ndups=1, block=biolrep) fit <- lmFit(MAAq, block=biolrep, cor=corfit$consensus) Error in gls.series(y, design = design, ndups = ndups, spacing = spacing, : Length of block does not match number of arrays Thank you for looking over this case. I?m struggling with the R program in general, so perhaps that accounts for some of my general confusion. Sincerely, Heather de Glanville

Dear Heather, You can't combine blocking and single-channel analysis in limma, at least not yet. Also, the single channel analysis is done by lmscFit() not lmFit(), hence the error message. Best wishes Gordon > Date: Mon, 02 Apr 2007 10:21:38 -0700 > From: Heather de Glanville <deglanvi at="" pdx.edu=""> > Subject: [BioC] Dup correlation in single-channel analysis?- technical > rep > To: bioconductor at stat.math.ethz.ch > > Dear Bioconductor, > > I am working with a loop design with both biological and technical > replication, and am having difficulty incorporating both types of > replication appropriately. I am looking at the both strain and the > treatment level effects, will make most all possible contrasts, and > would like to test this over the biorep error. > > My experiment follows, with 6 different strain/treatments > (CD,CW,HD,HW,VD,VW), 3 bio reps per strain/treat (1,2,3) and 2 techreps > per biorep. > [targets frame deleted] > > It seems like I could use single-channel analysis, and use duplicate > correlation to indicate which file and channels are the technical reps. > I am getting an error when attempting to do this > > targets2 <- targetsA2C(targets) > u <- unique(targets2$Target) > f <- factor(targets2$Target, levels=u) > design <- model.matrix(~0+f) > colnames(design) <- u > biolrep > <-c(11,18,7,11,10,8,8,15,9,1,12,4,13,17,16,14,14,3,17,6,18,10,15,9,1 ,5,2,7,4,2,5,16,3,13,6,12) > corfit <-duplicateCorrelation(MAAq, ndups=1, block=biolrep) > fit <- lmFit(MAAq, block=biolrep, cor=corfit$consensus) > > Error in gls.series(y, design = design, ndups = ndups, spacing = spacing, : > > Length of block does not match number of arrays > > Thank you for looking over this case. I?m struggling with the R program > in general, so perhaps that accounts for some of my general confusion. > > Sincerely, > > Heather de Glanville