[BioC] Yet another nested design in limma

[Naomi Altman]

You can design this in limma quite 
readily.  Nesting really just means that only a 
subset of the possible contrasts are of 
interest.  Just create the appropriate contrast matrix and you are all set.

--Naomi

At 12:08 PM 2/16/2009, Paolo Innocenti wrote:
>Hi all,
>
>I have an experimental design for a Affy experiment that looks like this:
>
>         Phen    Line    Sex     Biol.Rep.
>File1   H       1       M       1
>File2   H       1       M       2
>File3   H       1       F       1
>File4   H       1       F       2
>File5   H       2       M       1
>File6   H       2       M       2
>File7   H       2       F       1
>File8   H       2       F       2
>File9   L       3       M       1
>File10  L       3       M       2
>File11  L       3       F       1
>File12  L       3       F       2
>File13  L       4       M       1
>File14  L       4       M       2
>File15  L       4       F       1
>File16  L       4       F       2
>
>
>This appears to be a slightly more complicated 
>situation than the one proposed in the section 
>8.7 of the limma users guide (p.45) or by Jenny on this post:
>
>https://stat.ethz.ch/pipermail/bioconductor/2006-February/011965.html
>
>In particular, I am intersted in
>- Effect of "sex" (M vs F)
>- Interaction between "sex" and "phenotype ("line" nested)
>- Effect of "phenotype" in males
>- Effect of "phenotype" in females
>
>Line should be nested in phenotype, because they 
>are random "strains" that happened to end up in phenotype H or L.
>
>Can I design this in limma? Is there a source of 
>information about how to handle with this? In 
>particular, can I design a single model matrix 
>and then choose the contrasts I am interested in?
>
>Any help is much appreciated,
>paolo
>
>
>--
>Paolo Innocenti
>Department of Animal Ecology, EBC
>Uppsala University
>Norbyvägen 18D
>75236 Uppsala, Sweden
>
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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)
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