[BioC] limma lmFit error

[J.delasHeras at ed.ac.uk]

I think it means you stated that "D2R" was your reference, as in a  
common reference design, where every slide uses that same reference,  
but your design is not like that: your D4 and D7 samples are  
completely unlinked to D2R, therefore limma can only estimate D2.

You may want to look at Chapter 9 in the limma users guide (single  
channel analysis of two-color data), p50.

Jose

Quoting Ben Nota <ben.nota at ecology.falw.vu.nl>:

> 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/
>
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>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK