On Aug 28, 2011, at 11:37 AM, Ram H. Sharma wrote:
Dear R users:
Sorry for this simple question:
I am writing a function where I would need to pickup p values and make
-log10 of it.
The p values are from an anova output and sometime it can yield me 0.
-log10 (0)
[1] Inf
I can not replace Inf with 0, which not case here.
Well you could, but if you did, you would be shooting yourself in the
foot.
This is restricting me to go further in the function and out me the
error.
You help is highly appreciated.
I would think that one would be better served , not by trying to
redefine the log of small numbers, but rather by first putting a
lowering bound on the p-values.
pvec.trimmed <- pmax(pvec, 0.0000001)
min(log10(pvec.trimmed)) # now would be -7
The alternative that you suggest would be putting all of the p-values
of 0 in the same locations as the p-values of 1 after log
transformation. That cannot be a wise idea. Rather like redefining pi
to be 3.14.
--
David Winsemius, MD
West Hartford, CT
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