[R] about a p-value < 2.2e-16

[Bogdan Tanasa]

Dear Peter, thanks a lot. yes, we can see a very precise p-value, and that
was the request from the journal.

if I may ask another question please : what is the meaning of "exact=TRUE"
or "exact=FALSE" in wilcox.test ?

i can see that the "numerically precise" p-values are different. thanks a
lot !

tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
tst$p.value
[1] 8.535524e-25

tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=FALSE)
tst$p.value
[1] 3.448211e-25

On Thu, Mar 18, 2021 at 10:15 PM Peter Langfelder <
peter.langfelder using gmail.com> wrote:

> I thinnk the answer is much simpler. The print method for hypothesis
> tests (class htest) truncates the p-values. In the above example,
> instead of using
>
> wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
>
> and copying the output, just print the p-value:
>
> tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
> tst$p.value
>
> [1] 2.988368e-32
>
>
> I think this value is what the journal asks for.
>
> HTH,
>
> Peter
>
> On Thu, Mar 18, 2021 at 10:05 PM Spencer Graves
> <spencer.graves using effectivedefense.org> wrote:
> >
> >        I would push back on that from two perspectives:
> >
> >
> >              1.  I would study exactly what the journal said very
> > carefully.  If they mandated "wilcox.test", that function has an
> > argument called "exact".  If that's what they are asking, then using
> > that argument gives the exact p-value, e.g.:
> >
> >
> >  > wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
> >
> >          Wilcoxon rank sum exact test
> >
> > data:  rnorm(100) and rnorm(100, 2)
> > W = 691, p-value < 2.2e-16
> >
> >
> >              2.  If that's NOT what they are asking, then I'm not
> > convinced what they are asking makes sense:  There is is no such thing
> > as an "exact p value" except to the extent that certain assumptions
> > hold, and all models are wrong (but some are useful), as George Box
> > famously said years ago.[1]  Truth only exists in mathematics, and
> > that's because it's a fiction to start with ;-)
> >
> >
> >        Hope this helps.
> >        Spencer Graves
> >
> >
> > [1]
> > https://en.wikipedia.org/wiki/All_models_are_wrong
> >
> >
> > On 2021-3-18 11:12 PM, Bogdan Tanasa wrote:
> > >   <
> https://meta.stackexchange.com/questions/362285/about-a-p-value-2-2e-16>
> > > Dear all,
> > >
> > > i would appreciate having your advice on the following please :
> > >
> > > in R, the wilcox.test() provides "a p-value < 2.2e-16", when we compare
> > > sets of 1000 genes expression (in the genomics field).
> > >
> > > however, the journal asks us to provide the exact p value ...
> > >
> > > would it be legitimate to write : "p-value = 0" ? thanks a lot,
> > >
> > > -- bogdan
> > >
> > >       [[alternative HTML version deleted]]
> > >
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> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

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