Dear All:
I just started getting familiar with the use of R and different packages to analyze liver samples. After some reading and searching I was able to understand how to pre-process the data including normalization with GCRMA but now I got a problem when using LIMMA and trying to built my design.
I have 18 arrays, a group of 6 are from liver of calves that were born from dams fed 3 different diets (Damdiet: Ctl, SFA, EFA). After the calves were born, a group of 3 from each dam diet were fed 2 different milk replacers (MR: LLA, HLA). So I have a factorial (3x2). I am interested in evaluating specific orthogonal contrast and I couldn't find any online help about how I can set the model matrix in limma for those contrast of interest.
As if I were to use my orthogonal contrast in SAS they would be:
contrast 'Ctl vs (SFA+EFA)' Damdiet -2 1 1;
contrast 'EFA vs SFA' damdiet 0 -1 1;
contrast 'MR' MR -1 1;
contrast 'MR by ctl vs (SFA+EFA)' MR*damdiet 2 -1 -1 -2 1 1;
contrast 'MR by EFAvs SFA' calfdiet*damdiet 0 1 -1 0 -1 1;

I will deeply appreciate any help.
Miriam


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Miriam Garcia, MS
PhD candidate
Department of Animal Sciences
University of Florida

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