Dear all,


I was wondering why there is so many difference between the two following approaches  to handle the replication for my experiments - therefore, I don't which one to trust.


briefly, Here is my target :
Cy3	Cy5
wt1	mu1
mu1	wt1
wt2	mu2
mu2	wt2
wt3	mu3
mu3	wt3


to get the gene differentially expressed between Mutant and WT, I have stricly followed the two solutions given in the page 37 of limma userguide (3rd apriol 2010):
- the first one (page 37) is using duplicateCorrelation
- the second one clearly explicit the design matrix and the contrast matrix (page 38) as follow

design = cbind(
		R1_MuvsWT = c(-1,1,0,0,0,0),
		R2_MuvsWT = c(0,0,-1,1,0,0),
		R3_MuvsWT = c(0,0,0,0,-1,1)
)
fit = lmFit(MAn,design)

cont.matrix = makeContrasts (
		MuvsWT = (R1_MuvsWT + R2_MUvsWT+R3_MUvsWT)/3,
		levels = design
)


using these two approaches give quantitatively different results.


Which one should I trust ?

Thanks by advance for any pieces of advice and / or any help

Cheers

--
G.M
--
Guillaume Meurice - PhD
Bioinformaticien

Unité de Génomique Fonctionnelle 

PR2 - Bureau 323.2
Poste : 3509

Institut Gustave Roussy - PR2
114 rue Edouard Vaillant - 94805 VILLEJUIF Cedex
tel	: +33 (0)1 42 11 42 11 (poste 3509)
fax	: +33 (0)1 42 11 62 67


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