[BioC] Limma Factorial design for two color data

Naomi Altman naomi at stat.psu.edu
Sun Nov 2 16:23:20 CET 2008

I generally find it easier to do a single channel analysis for these 
more complicated designs.  Just follow the manual for single channel 
and you can then use the treatments directly to form the contrasts.


At 12:14 PM 10/31/2008, Adrian Johnson wrote:
>Hi :
>sorry for re-sending the my question. Lookinf forward for some help. thanks.
>I searched bioconductor list archive and could not find appropriate
>modelmatrix and contrast matrix fitting
>for the following type of data from two color.
> > targets
>    Array Cy3 Cy5 Treatment Shock
>1 Array1  WT  MU         Y     H
>2 Array2  WT  MU         N     C
>3 Array3  WT  MU         Y     H
>4 Array4  MU  WT         N     C
>5 Array5  WT  MU         Y     C
>6 Array6  WT  MU         Y     C
>I want to compare (MU.WT-Y) - (MU.WT-N)
>and (MU.WT-H)-(MU.WT-C)
>How can I design my model matrix and fit contrasts.
>Could some one help me please.
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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