[BioC] Interaction terms on a factorial design without a reference sample
blemos at oeb.harvard.edu
Wed May 23 04:56:02 CEST 2007
I am analyzing an experiment with two-color arrays in which
expression data was collected from two genotypes in two different
environments according to a loop design. I wanted to use LIMMA to
test for effects due to genotype, environment, and their interaction.
The LIMMA user's guide has a good example on a similar factorial
design which includes, in addition to the four treatments of
interest, an external fifth RNA source used as a reference. I don't
have such a reference in my design and am having a hard time coding
for the design matrix such that I can make the contrasts between
genotypes (1&2), between environments (1&2), and also have an term
for the interaction of genotypes and environments.
Below is a scheme of the design, with lines being dye-swap
genotype_1_Environment_1 ---------- genotype_1_Environment_2
genotype_2_Environment_1 ---------- genotype_2_Environment_2
Any ideas on how to code for the design matrix in such a case?
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