# [BioC] Problems making contrasts

James W. MacDonald jmacdon at med.umich.edu
Thu Feb 21 16:37:15 CET 2008

```Hi Ingrid,

I haven't used makeContrasts() for a while now, so I'm not sure I can
help with that. However, it isn't difficult to construct your contrast
matrix by hand.

nam <- colnames(design)
contrast <- matrix(c(1,-1,0,0,0,0,1,-1,0.5,-0.5,0.5,-0.5), ncol = 3,
dimnames = list(nam,c(paste(nam[c(1,3)], nam[c(2,4)],
sep = "-"), "Stimulated-Unstimulated")))

You might get the same result by dividing by two in your call to
makeContrasts() rather than four.

Best,

Jim

Ingrid H. G. Østensen wrote:
> Hi
>
> I have some problems making my contrast matrix.
>
> I have the following design matrix:
> 	P_s	P_us	D_s	D_us
> S1	1	0	0	0
> S2	1	0	0	0
> S3	0	1	0	0
> S4	0	1	0	0
> S5	0	0	1	0
> S6	0	0	1	0
> S7	0	0	0	1
> S8	0	0	0	1
>
>
> Where P = patiens and D = donor, s = stimulated and us = unstimulated
>
> What I want is to find the following differences:
> The differences between stimulated and unstimulated in the patients group, and the differences between stimulated and unstimulated in the donor group. This I am able to make, the two first contrasts.
>
> But then I also want to see the difference between the two treatmens undepended of samples: stimulated vs unstimulated.
> In other words: (P_s and D_s) vs (P_us and D_us). Is my last contrast correct or should I do something else?
>
> contrast.matrix <-
> makeContrasts(P_s-P_us, D_s-D_us, (P_s-P_us + D_s-D_us)/4, levels = designMa)
>
> Regards,
> Ingrid
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

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