The chosen method for selecting items using the limma package: "quadratic" for
a quadratic trend test on dose ranks, "linear" for a linear trend test on dose
ranks and "ANOVA" for an ANOVA-type test.
The ANOVA_based test ("ANOVA") is classically used for selection of omics data
in the general case but it requires many replicates per dose to be efficient,
and is thus not really suited for a dose-response design.
The linear trend test ("linear") aims at detecting monotonic trends from
dose-response designs, whatever the number of replicates per dose.
As proposed by Tukey (1985), it tests the global significance of a linear
model describing the response as a function of the dose in rank-scale.
The quadratic trend test ("quadratic") tests the global significance of a
quadratic model describing the response as a function of the dose in rank-scale.
It is a variant of the linear trend method that aims at detecting monotonic and
non monotonic trends from a dose-response designs, whatever the number of
replicates per dose (default chosen method).
We recommend the use of the latter for selecting both monotonic
and biphasic trends form a dose-response design.
For details, see
Tukey JW, Ciminera JL and Heyse JF (1985).
Testing the statistical certainty of a response to increasing doses of a drug.
Biometrics, 295-301.