[BioC] Help with

[Guillaume Meurice]

Sorry, I made some mistake in my previous mail, into the contrast matrix (bad copy paste from another project), so here I have corrected them.

> I have a question regarding the way to properly design biological replicate and technical replicates.
> 
> In the projet, we have two groups of sample : R (respond to the treatment), NR (no response).
> For each groups, there is several replicates (3) that come from different patients (so not strictely biological).
> Each patient have two sample : one at day one(d1), the second after one week (d7)
> The hybridization are planned to be performed in dual color, with dye-sap.
> 
> Here is the target file :
> 
> Cy3	Cy5	Patient	Issu	TechnicalReplicat
> d1	d7	A	R	1
> d7	d1	A	R	1
> d1	d7	B	R	2
> d7	d1	B	R	2
> d1	d7	C	R	3
> d7	d1	C	R	3
> d1	d7	D	NR	4
> d7	d1	D	NR	4
> d1	d7	E	NR	5
> d7	d1	E	NR	5
> d1	d7	F	NR	6
> d7	d1	F	NR	6
> 
> 
> my question is how to properly design the matrix design and the contrast matrix to answer the difference between the two groups ?
> Which column should I use as biological replicat (so as I can use the duplicateCorrelation function) ?
> 
> here is how I've started, but I can't figure out how to use duplicateCorrelation with this design
> 
> design <- cbind(
> 		R_D7vsD1  = c(-1,1,-1,1,-1,1,  0,0, 0,0, 0,0),
> 		NR_D7vsD1 = c( 0,0,0,0,0,0,-1,1,-1,1,-1,1)
> )
> fit <- lmFit(MAn, design, weights = NULL)
> cont.mat = makeContrasts(NRvsR = NR_D7sD1 - R_D7vsD1, levels = design)
> fit2 <- contrasts.fit(fit, cont.mat)
> fit2 <- eBayes(fit2)
> 
> 
> 
> 
> Many thanks by advance for any help.
> 
> --
> Guillaume
> 	[[alternative HTML version deleted]]
> 
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