Hi, I am using the Limma package and I am getting warnings when trying to fit a linear model to my data in an "MAList", using a vector of weights (0 or 1) to discount genes that do not pass the low intensity filter in *all* my arrays. I made a little example with made up data here that reproduces teh warnings: # Make an MAList with 3 columns of 100 genes: MA3<-new("MAList") MA3$M<-matrix(rnorm(300), ncol=3) MA3$A<-matrix(abs(rnorm(300)), ncol=3) # create a weights vector, all 1 except for three elements turned to 0. low3<-rep(1, times=100) low3[c(10, 50, 90)]<-0 # no dye swap, straight replicates design<-c(1,1,1) # running the following command (no weights) works ok: fit<-lmFit(MA3, design=design, weights=NULL) # ok # if I try to use the weights, I get a warning: fit<-lmFit(MA3, design=design, weights=low3) # warnings Warning message: In lmFit(MA3, design = design, weights = low3) : Some coefficients not estimable: coefficient interpretation may vary. but the coefficients for the zero weighted elements are NA, however. What is the reason for the warning? Shall I be concerned? In my actual data about 25% of the genes are weighted zero. This is my sessionInfo(): > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] limma_2.14.0 svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5 svIDE_0.9-5 loaded via a namespace (and not attached): [1] tools_2.7.0 > Jose -- 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 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.