contrasts.fit Error
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Matt McCall ▴ 50
@matt-mccall-926
Last seen 6.9 years ago
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$M, cln.mm) where colon is a limma object and cln.mm is the model matrix. also cln.cm is the contrast matrix from: cln.cm <- makeContrasts(MSLiver-MSLung, MSLiver-MSLiverLung, MSLung-MSLiverLung, levels=cln.mm) I get the error: Error in o %*% RUC^2 : non-conformable arguments Can anyone tell me what I'm doing wrong? I'm running: Package: limma Version: 1.7.0 Date: 2004/06/27 Title: Linear Models for Microarray Data Author: Gordon Smyth <smyth@wehi.edu.au>, Matt Ritchie <mritchie@wehi.edu.au>, James Wettenhall <wettenhall@wehi.edu.au>, Natalie Thorne <thorne@wehi.edu.au> Maintainer: Gordon Smyth <smyth@wehi.edu.au> Depends: R (>= 1.7.1), MASS, splines, statmod (>= 1.0.6), sma Description: Data analysis, linear models and differential expression for microarray data. License: LGPL URL: http://bioinf.wehi.edu.au/limma/ Packaged: Tue Jun 29 21:38:42 2004; madman Built: R 2.0.0; ; 2004-06-30 13:15:39; windows platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major 1 minor 9.1 year 2004 month 06 day 21 language R Microarray Colon limma Microarray Colon limma • 809 views ADD COMMENT 0 Entering edit mode @gordon-smyth Last seen 17 minutes ago WEHI, Melbourne, Australia We have seen this error message previously when the design matrix was singular and people attempted to take contrasts of non-estimable coefficients. There was a fix introduced in limma 1.7.5 to warn about non-singular design matrices and to catch this problem in contrasts.fit(). Try updating limma and see if the above turns out to be the problem. It is easiest to update limma directly from CRAN, just typing > install.packages("limma") should do it. Gordon > When I try to run the following line of code: > cln.fit2 <- contrasts.fit(cln.fit, cln.cm) > where cln.fit comes from: > cln.fit <- lmFit(colon$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
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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 > ADD REPLY 0 Entering edit mode 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 >