Entering edit mode
Nolwenn Le Meur
▴
30
@nolwenn-le-meur-888
Last seen 10.5 years ago
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
Facult? de m?decine
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44035 Nantes Cedex 1
France
Tel: (+33)-2-40-41-29-86 (office)
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mail: nolwenn.lemeur@nantes.inserm.fr