[BioC] contrasts.fit Error

Gordon K Smyth smyth at wehi.EDU.AU
Fri Sep 24 17:22:33 CEST 2004


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 at wehi.edu.au>, Matt Ritchie
> <mritchie at wehi.edu.au>, James Wettenhall <wettenhall at wehi.edu.au>,
> Natalie Thorne
>                  <thorne at wehi.edu.au>
> Maintainer: Gordon Smyth <smyth at 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



More information about the Bioconductor mailing list