You design matrix singular. If you run lmFit() it will warn you that coefficient I is non-estimable. Gordon > I updated my version and still get the same error. Here is the model > matrix if that helps: > cln.mm > A B C D E F H I J > 1 0 0 0 1 0 1 0 0 0 > 2 0 0 0 1 1 0 0 0 0 > 3 1 0 0 0 0 1 0 0 0 > 4 0 0 1 0 0 0 0 1 0 > 5 0 0 1 0 0 0 0 1 0 > 6 0 0 0 1 0 1 0 0 0 > 7 1 0 0 0 1 0 0 0 0 > 8 0 0 0 1 1 0 0 0 0 > 9 1 0 0 0 0 0 1 0 0 > 10 0 0 1 0 0 0 0 1 0 > 11 1 0 0 0 1 0 0 0 0 > 12 0 1 0 0 0 0 0 1 0 > 13 0 1 0 0 0 1 0 0 0 > 14 1 0 0 0 1 0 0 0 0 > 15 1 0 0 0 0 0 0 1 0 > 16 0 0 1 0 0 0 0 1 0 > 17 0 0 0 1 1 0 0 0 0 > 18 1 0 0 0 0 0 1 0 0 > 19 1 0 0 0 0 0 1 0 0 > 20 0 0 0 1 1 0 0 0 0 > 21 1 0 0 0 1 0 0 0 0 > 22 0 0 0 1 1 0 0 0 0 > 23 0 0 0 1 0 0 1 0 0 > 24 0 0 0 1 0 0 1 0 0 > 25 0 0 1 0 0 0 0 1 0 > 26 0 0 0 1 0 0 1 0 0 > 27 1 0 0 0 1 0 0 0 0 > 28 1 0 0 0 0 0 1 0 0 > 29 0 0 1 0 0 0 0 1 0 > 30 1 0 0 0 0 0 1 0 0 > 110 0 0 1 0 1 0 0 0 1 > 210 0 0 1 0 1 0 0 0 1 > 31 1 0 0 0 0 1 0 0 1 > 41 1 0 0 0 0 0 0 1 1 > 51 1 0 0 0 0 0 0 1 1 > 61 0 1 0 0 0 1 0 0 1 > 71 0 0 0 1 0 0 0 1 1 > 81 1 0 0 0 1 0 0 0 1 > 91 0 1 0 0 0 0 1 0 1 > 101 1 0 0 0 0 0 0 1 1 > 111 1 0 0 0 0 1 0 0 1 > 121 0 1 0 0 1 0 0 0 1 > 131 0 1 0 0 0 1 0 0 1 > 141 1 0 0 0 1 0 0 0 1 > 151 0 1 0 0 1 0 0 0 1 > 161 0 1 0 0 0 0 1 0 1 > 171 1 0 0 0 1 0 0 0 1 > 181 0 1 0 0 1 0 0 0 1 > 191 0 1 0 0 1 0 0 0 1 > 201 1 0 0 0 0 0 0 1 1 > 211 0 1 0 0 0 1 0 0 1 > 221 0 1 0 0 0 0 0 1 1 > 231 1 0 0 0 0 0 0 1 1 > > cln.cm <- makeContrasts(A-B, A-C, B-C, levels=cln.mm) > cln.fit2 <- contrasts.fit(cln.fit, cln.cm) > > I'm now running limma version 1.7.7 > Thanks for any help you can give. > Matt > > On Sep 24, 2004, at 11:22 AM, Gordon K Smyth wrote: > >> We have seen this error message previously when the design matrix was >> singular and people >> attempted to take contrasts of non-estimable coefficients. There was >> a fix introduced in limma >> 1.7.5 to warn about non-singular design matrices and to catch this >> problem in contrasts.fit(). >> >> Try updating limma and see if the above turns out to be the problem. >> It is easiest to update >> limma directly from CRAN, just typing >> >>> install.packages("limma") >> >> should do it. >> >> Gordon >> >>> When I try to run the following line of code: >>> cln.fit2 <- contrasts.fit(cln.fit, cln.cm) >>> where cln.fit comes from: >>> cln.fit <- lmFit(colon$M, cln.mm) >>> where colon is a limma object and cln.mm is the model matrix. >>> also cln.cm is the contrast matrix from: >>> cln.cm <- makeContrasts(MSLiver-MSLung, MSLiver-MSLiverLung, >>> MSLung-MSLiverLung, levels=cln.mm) >>> >>> I get the error: >>> Error in o %*% RUC^2 : non-conformable arguments >>> >>> Can anyone tell me what I'm doing wrong? >>> >>> I'm running: >>> Package: limma >>> Version: 1.7.0 >>> Date: 2004/06/27 >>> Title: Linear Models for Microarray Data >>> Author: Gordon Smyth <smyth@wehi.edu.au>, Matt Ritchie >>> <mritchie@wehi.edu.au>, James Wettenhall <wettenhall@wehi.edu.au>, >>> Natalie Thorne >>> <thorne@wehi.edu.au> >>> Maintainer: Gordon Smyth <smyth@wehi.edu.au> >>> Depends: R (>= 1.7.1), MASS, splines, statmod (>= 1.0.6), sma >>> Description: Data analysis, linear models and differential expression >>> for microarray data. >>> License: LGPL >>> URL: http://bioinf.wehi.edu.au/limma/ >>> Packaged: Tue Jun 29 21:38:42 2004; madman >>> Built: R 2.0.0; ; 2004-06-30 13:15:39; windows >>> >>> platform powerpc-apple-darwin6.8 >>> arch powerpc >>> os darwin6.8 >>> system powerpc, darwin6.8 >>> status >>> major 1 >>> minor 9.1 >>> year 2004 >>> month 06 >>> day 21 >>> language R >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >