[BioC] limma troncated design matrix

[Nolwenn Le Meur]

Hi everyone,

I'm trying to test the effect of different medical parameters (fators) on my
data with limma but I get a troncated design matrix.
I've two factors 'UNOS' and 'Etiology' (with 3 and 2 levels respectively)
listed below:

Target.txt file looks like:
sample	UNOS	Etiology
s1		1	CMD
s2		1	CAD
s3		1B	CMD
s4		1B	CAD
S5		2	CMD
S6		2	CAD
...

I reading it as a phenoData file.

I would like to know the different effects so I create a design matrix:

>design<-model.matrix(~-1+Etiology*UNOS,data=pData(target))
>design
EtiologyCAD	EtiologyCMD	UNOS1B UNOS2 EtiologyCAD:UNOS1B EtiologyCAD:UNOS2
EtiologyCMD:UNOS1B EtiologyCMD:UNOS2

but UNOS1 factor level is missing in the design matrix, Am I doing something
wrong ?

Thanks,

Nolwenn


********************************************
Nolwenn Le Meur
INSERM U533
Faculté de médecine
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