R help - Nov 2003 - FDR in p.adjust

Hello,

I've a question about the fdr method in p.adjust: What is the threshold of
the FDR, and is it possible to change this threshold?

As I understand the FDR (please correct) it adjusts the p-values so that for
less than N% (say the cutoff is 25%) of the alternative hypothesis the Null
is in fact true.

	thanks a lot for help,
	+regards,

	Arne

There is no threshold for fdr. The adjusted p-values give the expected
proportion of false positives for all comparisons with similar p-values
or smaller. In other words, if you choose a p-value of 0.05, you would
expect that ~5% of the tests with a p-value of 0.05 or smaller are false
positives.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> <Arne.Muller at aventis.com> 11/03/03 10:33AM >>>
Hello,

I've a question about the fdr method in p.adjust: What is the threshold
of
the FDR, and is it possible to change this threshold?

As I understand the FDR (please correct) it adjusts the p-values so
that for
less than N% (say the cutoff is 25%) of the alternative hypothesis the
Null
is in fact true.

	thanks a lot for help,
	+regards,

	Arne

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