33superwoman

The aim of the moderated t-test is to test whether the log-ratios are consistently greater or lesser than zero, not to test whether the log-ratios are equal.  The moderated t-test does not penalize a gene for having a large variance as much as the ordinary t-test would do.  Compared to the ordinary t-test, the moderated t-test gives more weight to the treatment fold change.  It can therefore be viewed as a compromise between the ordinary t-test and ranking by fold-change.
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The basic difference between linear models and glms is that with linear models, the F-test and all the individual t-tests that make it up can be conducted as one computation, but for glms each individual 1df test and overall F-test have to all be separate computations.
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Delta beta refers to change in Beta value relative to a group.
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Pearson correlations are a marginal measure of association and thus sensitive to confounding factors.
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Agilent arrays - can't use robust-spline normalization, only global loess normalization is meaningful.