I have a very simple design: it has 2 tissues (saline vs ecoli injected), 2 time-point evaluation (24 hr and 48 hr post injection) with 2 observations per experimental unit (2 reps). We are using Affymetrix genechip arrays (mouse expression set 430A), so it makes a total of 8 arrays. It is a very simple ANOVA that I am trying to analyze using the R-package. I am using a UNIX SunOS 5.8, Solaris 8.0. I have followed the LIMMA vignette, and I got this error message: "No residual degrees of freedom in linear model fits". These are the commands that I used: ********************************************************************** ** ************** Limma 11/24/03 (did not work why?): > The usual: change directory in R-window > library(affy) > Data <- ReadAffy() > Data > eset <- expresso(Data,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") > exprs(eset) ## runs for awhile, 5 minutes for 22K probesets. > design <- model.matrix(~ -1+factor(c(1,2,1,2,3,4,3,4))) ## I have array1-8 (4 RNAs and 2 reps) > colnames(design) <- c("group1", "group2", "group3", "group4") ## I assume the groups refer to RNAs > library(limma) > fit <- lmFit(eset, design) ## works here > contrast.matrix <- makeContrasts(group2-group1, group4-group3, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) ## here I got error messages "no residual df in model fits" ********************************************************************** ** ************************************************************* I would appreciate having some help on solving this problem. Thanks a lot. Roger Roger L. Vallejo, Ph.D. Assist. Professor of Genomics/Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science Genomics & Bioinformatics Laboratory 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> Website: http://genomics.cas.psu.edu/ <http: genomics.cas.psu.edu=""/> [[alternative HTML version deleted]]

There is a bug in the version of limma that you are using. Update to the developmental version, and you should be fine. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Roger Vallejo" <rvallejo@psu.edu> 11/26/03 2:12 PM >>> I have a very simple design: it has 2 tissues (saline vs ecoli injected), 2 time-point evaluation (24 hr and 48 hr post injection) with 2 observations per experimental unit (2 reps). We are using Affymetrix genechip arrays (mouse expression set 430A), so it makes a total of 8 arrays. It is a very simple ANOVA that I am trying to analyze using the R-package. I am using a UNIX SunOS 5.8, Solaris 8.0. I have followed the LIMMA vignette, and I got this error message: "No residual degrees of freedom in linear model fits". These are the commands that I used: ********************************************************************** ** ************** Limma 11/24/03 (did not work why?): > The usual: change directory in R-window > library(affy) > Data <- ReadAffy() > Data > eset <- expresso(Data,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") > exprs(eset) ## runs for awhile, 5 minutes for 22K probesets. > design <- model.matrix(~ -1+factor(c(1,2,1,2,3,4,3,4))) ## I have array1-8 (4 RNAs and 2 reps) > colnames(design) <- c("group1", "group2", "group3", "group4") ## I assume the groups refer to RNAs > library(limma) > fit <- lmFit(eset, design) ## works here > contrast.matrix <- makeContrasts(group2-group1, group4-group3, levels=design) > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) ## here I got error messages "no residual df in model fits" ********************************************************************** ** ************************************************************* I would appreciate having some help on solving this problem. Thanks a lot. Roger Roger L. Vallejo, Ph.D. Assist. Professor of Genomics/Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science Genomics & Bioinformatics Laboratory 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> Website: http://genomics.cas.psu.edu/ <http: genomics.cas.psu.edu=""/> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor