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

[Vivek Das]

Hi Bogdan,

You can also get the information from the link of the Wilcox.test function
page.

“By default (if exact is not specified), an exact p-value is computed if
the samples contain less than 50 finite values and there are no ties.
Otherwise, a normal approximation is used.”

For more:

https://stat.ethz.ch/R-manual/R-devel/library/stats/html/wilcox.test.html

Hope this helps!

Best,

VD


On Thu, Mar 18, 2021 at 10:36 PM Bogdan Tanasa <tanasa using gmail.com> wrote:

> 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]]
> > > >
> > > > ______________________________________________
> > > > 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.
> > >
> > > ______________________________________________
> > > 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.
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>
-- 
----------------------------------------------------------

Vivek Das, PhD

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