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 <vd4mm...@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 <tan...@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.langfel...@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.gra...@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@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@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@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]] ______________________________________________ R-help@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.
