[BioC] limma lmFit error

[Ben Nota]

Dear BioC,

I'm getting an error using the lmFit function within limma. I'm using R 
2.4.0 with limma version 2.9.1.

A little background about the experiment:

I use two color agilent arrays containing duplicate spots. I have metal 
exposure compared to non exposed (= reference) at 3 different time 
points (2, 4 and 7 days). Four bio-replicates per time point.

Explanation of RNA sample names: Day 2 reference (D2R) vs. Day 2 Metal 
(D2M), Day 4 reference (D4R) vs. Day 4 Metal (D4M), etc.

I normalized my data using loess

My targets look like this:

 > targets
      Array     FileName Cy3 Cy5     Date
1  Array15A Array15A.txt D4R D4M 31/01/07
2  Array15B Array15B.txt D4M D4R 31/01/07
3  Array17A Array17A.txt D4R D4M 31/01/07
4  Array17B Array17B.txt D4M D4R 31/01/07
5  Array46A Array46A.txt D7R D7M 31/01/07
6  Array46B Array46B.txt D7M D7R 31/01/07
7  Array47A Array47A.txt D7R D7M 31/01/07
8  Array47B Array47B.txt D7M D7R 31/01/07
9  Array10A Array10A.txt D2M D2R 17/10/06
10 Array11A Array11A.txt D2R D2M 17/10/06
11 Array12A Array12A.txt D2M D2R 16/11/06
12 Array12B Array12B.txt D2R D2M 16/11/06

My design:

 > design<-modelMatrix(targets,ref="D2R")
Found unique target names:
 D2M D2R D4M D4R D7M D7R
 > design
   D2M D4M D4R D7M D7R
1    0   1  -1   0   0
2    0  -1   1   0   0
3    0   1  -1   0   0
4    0  -1   1   0   0
5    0   0   0   1  -1
6    0   0   0  -1   1
7    0   0   0   1  -1
8    0   0   0  -1   1
9   -1   0   0   0   0
10   1   0   0   0   0
11  -1   0   0   0   0
12   1   0   0   0   0

And my correlation is calculated:

 > cor<-duplicateCorrelation(MA,design,ndups=2)
 > cor$consensus.correlation
[1] 0.8890682

But if I want to fit my linear model I'll get the following error message:

 > fit<-lmFit(MA, design, ndups=2,cor=cor$consensus.correlation)
Coefficients not estimable: D4R D7R
Error in dimnames(cov.coef) <- list(coef.names, coef.names) :
        length of 'dimnames' [1] not equal to array extent

Does anybody knows what this error means and what I'm doing wrong? I 
hope so!

Thanks in advance!

Best regards, Ben.

-- 
Benjamin Nota
Vrije Universiteit
Department of Animal Ecology
De Boelelaan 1085
1081 HV AMSTERDAM, The Netherlands
Tel:  +31 (0)20-5987217
Fax: +31 (0)20-5987123
ben.nota at falw.vu.nl

http://www.bio.vu.nl/do/