[BioC] contrasts.fit Error

[Matt McCall]

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 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
>