Dear BioC, I'm getting an error using the lmFit function within limma. I'm using R 2.4.0 with limma version 2.9.1. A little background about the experiment: I use two color agilent arrays containing duplicate spots. I have metal exposure compared to non exposed (= reference) at 3 different time points (2, 4 and 7 days). Four bio-replicates per time point. Explanation of RNA sample names: Day 2 reference (D2R) vs. Day 2 Metal (D2M), Day 4 reference (D4R) vs. Day 4 Metal (D4M), etc. I normalized my data using loess My targets look like this: > targets Array FileName Cy3 Cy5 Date 1 Array15A Array15A.txt D4R D4M 31/01/07 2 Array15B Array15B.txt D4M D4R 31/01/07 3 Array17A Array17A.txt D4R D4M 31/01/07 4 Array17B Array17B.txt D4M D4R 31/01/07 5 Array46A Array46A.txt D7R D7M 31/01/07 6 Array46B Array46B.txt D7M D7R 31/01/07 7 Array47A Array47A.txt D7R D7M 31/01/07 8 Array47B Array47B.txt D7M D7R 31/01/07 9 Array10A Array10A.txt D2M D2R 17/10/06 10 Array11A Array11A.txt D2R D2M 17/10/06 11 Array12A Array12A.txt D2M D2R 16/11/06 12 Array12B Array12B.txt D2R D2M 16/11/06 My design: > design<-modelMatrix(targets,ref="D2R") Found unique target names: D2M D2R D4M D4R D7M D7R > design D2M D4M D4R D7M D7R 1 0 1 -1 0 0 2 0 -1 1 0 0 3 0 1 -1 0 0 4 0 -1 1 0 0 5 0 0 0 1 -1 6 0 0 0 -1 1 7 0 0 0 1 -1 8 0 0 0 -1 1 9 -1 0 0 0 0 10 1 0 0 0 0 11 -1 0 0 0 0 12 1 0 0 0 0 And my correlation is calculated: > cor<-duplicateCorrelation(MA,design,ndups=2) > cor$consensus.correlation [1] 0.8890682 But if I want to fit my linear model I'll get the following error message: > fit<-lmFit(MA, design, ndups=2,cor=cor$consensus.correlation) Coefficients not estimable: D4R D7R Error in dimnames(cov.coef) <- list(coef.names, coef.names) : length of 'dimnames' [1] not equal to array extent Does anybody knows what this error means and what I'm doing wrong? I hope so! Thanks in advance! Best regards, Ben. -- Benjamin Nota Vrije Universiteit Department of Animal Ecology De Boelelaan 1085 1081 HV AMSTERDAM, The Netherlands Tel: +31 (0)20-5987217 Fax: +31 (0)20-5987123 ben.nota at falw.vu.nl http://www.bio.vu.nl/do/

I think it means you stated that "D2R" was your reference, as in a common reference design, where every slide uses that same reference, but your design is not like that: your D4 and D7 samples are completely unlinked to D2R, therefore limma can only estimate D2. You may want to look at Chapter 9 in the limma users guide (single channel analysis of two-color data), p50. Jose Quoting Ben Nota <ben.nota at="" ecology.falw.vu.nl="">: > Dear BioC, > > I'm getting an error using the lmFit function within limma. I'm using R > 2.4.0 with limma version 2.9.1. > > A little background about the experiment: > > I use two color agilent arrays containing duplicate spots. I have metal > exposure compared to non exposed (= reference) at 3 different time > points (2, 4 and 7 days). Four bio-replicates per time point. > > Explanation of RNA sample names: Day 2 reference (D2R) vs. Day 2 Metal > (D2M), Day 4 reference (D4R) vs. Day 4 Metal (D4M), etc. > > I normalized my data using loess > > My targets look like this: > > > targets > Array FileName Cy3 Cy5 Date > 1 Array15A Array15A.txt D4R D4M 31/01/07 > 2 Array15B Array15B.txt D4M D4R 31/01/07 > 3 Array17A Array17A.txt D4R D4M 31/01/07 > 4 Array17B Array17B.txt D4M D4R 31/01/07 > 5 Array46A Array46A.txt D7R D7M 31/01/07 > 6 Array46B Array46B.txt D7M D7R 31/01/07 > 7 Array47A Array47A.txt D7R D7M 31/01/07 > 8 Array47B Array47B.txt D7M D7R 31/01/07 > 9 Array10A Array10A.txt D2M D2R 17/10/06 > 10 Array11A Array11A.txt D2R D2M 17/10/06 > 11 Array12A Array12A.txt D2M D2R 16/11/06 > 12 Array12B Array12B.txt D2R D2M 16/11/06 > > My design: > > > design<-modelMatrix(targets,ref="D2R") > Found unique target names: > D2M D2R D4M D4R D7M D7R > > design > D2M D4M D4R D7M D7R > 1 0 1 -1 0 0 > 2 0 -1 1 0 0 > 3 0 1 -1 0 0 > 4 0 -1 1 0 0 > 5 0 0 0 1 -1 > 6 0 0 0 -1 1 > 7 0 0 0 1 -1 > 8 0 0 0 -1 1 > 9 -1 0 0 0 0 > 10 1 0 0 0 0 > 11 -1 0 0 0 0 > 12 1 0 0 0 0 > > And my correlation is calculated: > > > cor<-duplicateCorrelation(MA,design,ndups=2) > > cor$consensus.correlation > [1] 0.8890682 > > But if I want to fit my linear model I'll get the following error message: > > > fit<-lmFit(MA, design, ndups=2,cor=cor$consensus.correlation) > Coefficients not estimable: D4R D7R > Error in dimnames(cov.coef) <- list(coef.names, coef.names) : > length of 'dimnames' [1] not equal to array extent > > Does anybody knows what this error means and what I'm doing wrong? I > hope so! > > Thanks in advance! > > Best regards, Ben. > > -- > Benjamin Nota > Vrije Universiteit > Department of Animal Ecology > De Boelelaan 1085 > 1081 HV AMSTERDAM, The Netherlands > Tel: +31 (0)20-5987217 > Fax: +31 (0)20-5987123 > ben.nota at falw.vu.nl > > http://www.bio.vu.nl/do/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK