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

[Bogdan Tanasa]

thanks a lot, Vivek ! in other words, assuming that we work with 1000 data
points,

shall we use EXACT = TRUE, it uses the normal approximation,

while if EXACT=FALSE (for these large samples), it does not ?

On Thu, Mar 18, 2021 at 10:47 PM Vivek Das <vd4mmind using gmail.com> wrote:

> 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
>

	[[alternative HTML version deleted]]