Hi,
I am investigating the global gene expression response to a continuous
environmental covariate in two groups of individuals using limma.
I am interested in genes whose  expression is:
A) correlated with the covariate
B) differentially correlated with the covariate in the two groups of
individuals (Interaction of Group and Covariate)

In order to be able to set up the proper contrasts I split the Covariate in
two Vectors where one Vector contains only the samples with the lowest
level of the covariate
e.g.  CovBase = c(0,0,0,3,0,3,0,0)
and where the other vector contains all the samples with higher levels of
the covariate
e.g. Cov = c(34,2,5,0,5,0,2,34)
and set up a design matrix without intercept:

~ Group + CovBase + Cov


The contrasts I am testing are specified as follows:
Effect of Covariate: Cov-CovBase
Interaction of Group and Covariate: (GroupA-GroupB) - (Cov-CovBase)

Does this procedure makes sense ?

Thank you very much in advance

Moritz

-- 

*Moritz Heß
PhD Candidate
*
*Research associate
Forest Research Institute
of Baden Württemberg (FVA)
Wonnhalde 4
79100 Freiburg (Germany)

phone +49 761 4018 301*

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