Hi, I am trying to use arrayWeights on a design as follows: >design = model.matrix(~-1+phenotype+SID) Where SID refers to matched samples and phenotype as a cell phenotype obtained from those samples. I run array weights: >arrayw <- arrayWeights(eset, design = design, trace = TRUE) Coefficients not estimable: SIDC4 SIDP5 SIDSG7 Error in chol.default(Zinfo) : the leading minor of order 48 is not positive definite What does this error mean? Here is a summary of the samples. The phenotypes are labeled a through k. > colSums(design) a b c d e f g h i j k 3 4 4 4 4 5 5 5 5 5 5 SID129 SID139 SID92 SIDC1 SIDC2 SIDC3 SIDC4 SIDP1 SIDP2 SIDP3 SIDP4 4 3 4 1 1 1 1 2 2 2 2 SIDP5 SIDSG3 SIDSG4 SIDSG5 SIDSG6 SIDSG7 2 4 4 4 4 4 Thanks, Fraser > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] limma_2.16.4 RODBC_1.2-4 hgu133plus2cdf_2.3.0 [4] affy_1.20.2 Biobase_2.2.1 rcom_2.0-4 [7] rscproxy_1.0-12 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0