Download limma: Linear Models for Microarray Data User's Guide (Now

for example interpreting the number of DE genes as representing the strength of the contrast.
However users need to be aware that the number of DE genes for any particular contrasts
will depend on which other contrasts are tested at the same time. Hence one should include
only those contrasts which are closely related to the question at hand. Unnecessary contrasts
should be excluded as these would affect the results for the contrasts of interest. Another
more theoretical issue is that there is no theorem which proves that adjust.method="BH" in
combination with method="global" will correctly control the false discovery rate for combinations of negatively correlated contrasts, however simulations, experience and some theory
suggest that the method is safe in practice.
The "hierarchical" method offers power advantages when used with adjust.method="holm"
to control the family-wise error rate. However its properties are not yet well understood with
adjust="BH".
method="nestedF" has a more specialised aim to give greater weight to probes which are significance for two or more contrasts. Most multiple testing methods tend to underestimate the
number of such probes. There is some practical experience to suggest that method="nestedF"
gives less conservative results when finding probes which respond to several different contrasts
at once. However this method should still be viewed as experimental. It provides formal false
discovery rate control at the probe level only, not at the contrast level.
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