[BioC] Limma time course with two-color microarrays
Gordon K Smyth
smyth at wehi.EDU.AU
Thu Mar 15 12:17:59 CET 2007
> Date: Wed, 14 Mar 2007 10:19:32 -0800 (PST)
> From: "Sergio Barberan" <barberan at biology.ucsc.edu>
> Subject: [BioC] Limma time course with two-color microarrays
> To: bioconductor at stat.math.ethz.ch
>
> Dear list,
>
> It might be a really easy problem but I can not figure out how to do it.
>
> I'm trying to analyze a set of hybs of a time course experiment, where I
> used a loop design. I have six samples and no reference, I compare
> (1-2,2-3,3-4,4-5,5-6,6-1); each with dye swaps so I have 12 slides.
>
> By selecting sample 1 as my reference in modelMatrix, I get the following
> design matrix:
>
> 2 3 4 5 6
> 1 0 -1 1 0 0
> 2 0 0 -1 1 0
> 3 0 0 0 -1 1
> 4 1 0 0 0 -1
> 5 0 1 0 0 0
> 6 0 0 0 1 -1
> 7 0 1 -1 0 0
> 8 -1 0 0 0 1
> 9 1 0 0 0 0
> 10 0 0 1 -1 0
> 11 0 -1 0 0 0
> 12 -1 0 0 0 0
>
> My question is: How to use contrastMatrix to obtain the following
> comparisons: 1-2, 2-3, 3-4, 4-5, 5-6 and 6-1?
You just have to remember that each column of your design matrix is already a contrast vs 1. So
you need
cont.matrix <- makeContrasts(-2,2-3,3-4,4-5,5-6,6,levels=design)
HOWEVER, to make this work the column names of the your design matrix must start with a letter,
not a number. E.g., you need "Time2", "Time3" etc instead of "2", "3" etc.
> I know there is some information about Limma and time course experiments
> but that example uses one-color arrays so I'm confused about how to apply
> that to my experimental design.
The two colour is the same as the one-colour from this point.
Best wishes
Gordon
> Thanks in advance for any help,
> Sergio
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