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conservative than controlling the FDR. In order to avoid a lot
of false-positives, the signifi cance level for each
p
value is
reduced to account for the number of comparisons being
performed. Using the Bonferroni correction to control the
FWER, the
p
values of the
m
investigated proteins are
compared with a signifi cance level of 0.05/
m
instead of 0.05
to control an overall level of the type 1 error rate of 0.05. For
example, in a validation experiment of fi ve potential biomark-
ers, the
p
values of the individual
t
tests have to be lower than
0.05/5 = 0.01. However, if
m
is very large (as in the discovery
set), the Bonferroni correction is too stringent (i.e., the power
of the investigated test may be rather small), and therefore, the
control of the FDR should be applied.
Acknowledgments
We thank Sonja Zehetmayer for helpful comments.
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