Hi Ted,
yes this was the problem. Thank you very much.

best
idaios


On Wed, Jan 9, 2013 at 4:51 PM, Ted Harding <Ted.Harding@wlandres.net>wrote:

> Ah! You have aqssigned a parameter "equal.var=TRUE", and "equal.var"
> is not a listed paramater for t.test() -- see ?t.test :
>
>   t.test(x, y = NULL,
>     alternative = c("two.sided", "less", "greater"),
>     mu = 0, paired = FALSE, var.equal = FALSE,
>     conf.level = 0.95, ...)
>
> Try it instead with "var.equal=TRUE", i.e. in your code:
>   for(i in 1:k){
>     rv.t.pvalues[i] <- t.test(rv[i, 1:(c/2)], rv[i, (c/2+1):c],
>   ##equal.var=TRUE, alternative="two.sided")$p.value
>     var.equal=TRUE, alternative="two.sided")$p.value
>   }
>
> When I run your code with "equal.var", I indeed repeatedly see
> the deficient bin for the lowest P-values that you observed.
> When I run your code with "var.equal" I do not see it.
>
> The explanation is that, since "equal.var" is not a recognised
> parameter for t.test(), it has assumed the default value FALSE
> for var.equal, and has therefore (since it is a 2-sample test)
> adopted the Welch/Satterthwaite procedure:
>
>   var.equal: a logical variable indicating whether to treat
>     the two variances as being equal. If 'TRUE' then the
>     pooled variance is used to estimate the variance
>     otherwise the Welch (or Satterthwaite) approximation
>     to the degrees of freedom is used.
>
> This has the effect of somewhat adapting the test procedure to
> the data, so that extreme (i.e. small) values of P are even
> rarer than they should be.
>
> With best wishes,
> Ted.
>
> On 09-Jan-2013 13:24:59 Pavlos Pavlidis wrote:
> > Hi Ted,
> > thanks for the reply. I use a similar code which you can see below:
> >
> > k <- 10000
> > c <- 6
> > rv <- array(NA, dim=c(k, c) )
> > for(i in 1:k){
> >   rv[i,] <- rnorm(c, mean=0, sd=1)
> > }
> >
> > rv.t.pvalues <- array(NA, k)
> >
> > for(i in 1:k){
> >   rv.t.pvalues[i] <- t.test(rv[i, 1:(c/2)], rv[i, (c/2+1):c],
> > equal.var=TRUE, alternative="two.sided")$p.value
> > }
> >
> > hist(rv.t.pvalues)
> >
> > The histogram is this one:
> > *http://tinyurl.com/histogram-rt-pvalues-pdf
> >
> > *
> > *all the best
> > idaios
> > *
> >
> >
> > On Wed, Jan 9, 2013 at 12:29 PM, Ted Harding <Ted.Harding@wlandres.net
> >wrote:
> >
> >> On 09-Jan-2013 08:50:46 Pavlos Pavlidis wrote:
> >> > Dear all,
> >> > I observer a strange behavior of the pvalues of the t-test under
> >> > the null hypothesis. Specifically, I obtain 2 samples of 3
> >> > individuals each from a normal distribution of mean 0 and variance 1.
> >> > Then, I calculate the pvalue using the t-test (var.equal=TRUE,
> >> > samples are independent). When I make a histogram of pvalues
> >> > I see that consistently the bin of the smallest pvalues has a
> >> > lower frequency. Is this a known behavior of the t-test or it's
> >> > a kind of bug/random number generation problem?
> >> >
> >> > kind regards,
> >> > idaios
> >>
> >> Using the following code, I did not observe the behavious you describe.
> >> The histograms are consistent with a uniform distribution of the
> >> P-values, and the lowest bin for the P-values (when the code is
> >> run repeatedly) is not consistently lower (or higher, or anything
> >> else) than the other bins.
> >>
> >> ## My code:
> >> N <- 10000
> >> Ps <- numeric(N)
> >> for(i in (1:N)){
> >>   X1 <- rnorm(3,0,1) ; X2 <- rnorm(3,0,1)
> >>   Ps[i] <- t.test(X1,X2,var.equal=TRUE)$p.value
> >> }
> >> hist(Ps)
> >> ################################################
> >>
> >> If you would post the code you used, the reason why you are observing
> >> this may become more evident!
> >>
> >> Hoping this helps,
> >> Ted.
> >>
> >> -------------------------------------------------
> >> E-Mail: (Ted Harding) <Ted.Harding@wlandres.net>
> >> Date: 09-Jan-2013  Time: 10:29:21
> >> This message was sent by XFMail
> >> -------------------------------------------------
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > 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.
>
> -------------------------------------------------
> E-Mail: (Ted Harding) <Ted.Harding@wlandres.net>
> Date: 09-Jan-2013  Time: 14:51:04
> This message was sent by XFMail
> -------------------------------------------------
>

	[[alternative HTML version deleted]]


