thanks a lot, Jiefei ! and thanks to all for your time and comments !
have a good weekend !
On Fri, Mar 19, 2021 at 10:01 PM Jiefei Wang wrote:
> Hi Bogdan,
>
> I think the journal is asking about the exact value of the pvalue, it
> doesn't matter if it is from the exact distribution or norm
Hi Bogdan,
I think the journal is asking about the exact value of the pvalue, it
doesn't matter if it is from the exact distribution or normal
approximation. However, it does not make any sense to report such a small
pvlaue. If I was you, I would show the reviewers the exact pvalue they want
and g
Yes, Bogdan, that sounds *exactly* right. ;-) -- it runs out of memory
trying to calculate the exact permutation distribution. What you apparently
get with exact = FALSE is the exact answer( to within floating point
arithmetic's approximation) to a normal approximation.
... and furthermore...
I
Thank you Kevin, their wording is "Please note that the exact p value
should be provided, when possible, etc"
by "exact p-value" i believe that they do mean indeed the actual number,
and not to specify "exact=TRUE" ;
as we are working with 1000 genes, shall i specify "exact=TRUE" on my PC,
it run
I have to ask since. Are you sure the journal simply means by exact p-value
that they don’t want to see a p-value given as < 0.0001, for example, and
simply want the actual number?
I cannot imagine they really meant exact as in the p-value from some exact
distribution.
--
Kevin E. Thorpe
Head
Dear all, thank you all for comments and help.
as far as i can see, shall we have samples of 1000 records, only
"exact=FALSE" allows the code to run:
wilcox.test(rnorm(1000), rnorm(1000, 2), exact=FALSE)$p.value
[1] 7.304863e-231
shall i use "exact=TRUE", it runs out of memory on my 64GB RAM PC
For me, it was always clear based on the documentation that if there are ties,
then the normal approximation is used (irrespective of what 'exact' is set to).
In fact, if there are ties, the output even tells you that this is happening:
wilcox.test(c(1,3,2,2,4), exact=TRUE)
[...]
Warning messag
I **believe** -- if my old memory still serves-- that the "exact"
specification uses a home grown version of the algorithm to calculate
exact, or close approximations to the exact, permutation distribution
originally developed by Cyrus Mehta, founder of StatXact software. Of
course, examining the
Hi Spencer,
Thanks for your test results, I do not know the answer as I haven't
used wilcox.test for many years. I do not know if it is possible to compute
the exact distribution of the Wilcoxon rank sum statistic, but I think it
is very likely, as the document of `Wilcoxon` says:
This distributi
Dear Jiefei, and all,
many thanks for your time and comments, suggestions, insights.
-- bogdan
On Fri, Mar 19, 2021 at 7:52 AM Jiefei Wang wrote:
> After digging into the R source, it turns out that the argument `exact`
> has nothing to do with the numeric precision. It only affects the statis
Dear Wolfgang,
Thanks for the documentation, but the document only states the default
behavior, it does not mention what would happen if we tell it to compute
the exact p-value but the data has ties. I think this would be misleading
as people might think their result is exact by specifying `exact=
Dear Jiefei,
This behavior is documented. From help(wilcox.test):
"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."
Best,
Wolfgang
>-Original Message---
On 2021-3-19 9:52 AM, Jiefei Wang wrote:
After digging into the R source, it turns out that the argument `exact` has
nothing to do with the numeric precision. It only affects the statistic
model used to compute the p-value. When `exact=TRUE` the true distribution
of the statistic will be used.
After digging into the R source, it turns out that the argument `exact` has
nothing to do with the numeric precision. It only affects the statistic
model used to compute the p-value. When `exact=TRUE` the true distribution
of the statistic will be used. Otherwise, a normal approximation will be
use
Hey,
I just want to point out that the word "exact" has two meanings. It can
mean the numerically accurate p-value as Bogdan asked in his first email,
or it could mean the p-value calculated from the exact distribution of the
statistic(In this case, U stat). These two are actually not related, eve
On 2021-3-19 12:54 AM, Bogdan Tanasa wrote:
> 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 ?
As David Winsemius noted,
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