Rich Ulrich <[EMAIL PROTECTED]> wrote: > On 17 Oct 2003 06:05:19 -0700, [EMAIL PROTECTED] (Enda Kelly) > wrote:
> [ snip, discussion ] >> This was done for a number of pairs of loci. To illustrate what I meant >> by "narrow" and "enormous", here are some examples with the p-value, the >> median of the bootstrap values and the upper and lower limits of 95% CI: >> >> Locus pair P-value Median Lower Upper >> 1 0.002414 0.002422 0.000055 0.037401 > In terms of ratio: Big. > These are enormous, Median/Lower and Upper/Median. >> 2 0.971621 0.512296 0.181935 0.850761 > ? In terms of sanity, or a dysfunctional program: > Is this a typographical error, or is the point-estimate > outside of CI? >> 3 0.000000 0.000000 0.000000 0.000000 >> 4 0.018936 0.016100 0.001082 0.193285 > Ratios are again more than 10-fold, for size of p. >> 5 0.832001 0.505662 0.173286 0.857703 > ? Point estimate is within the CI, but not by much. >> >> Judging by the comments on the relationship between p-values and >> confidence intervals, I have a suspicion that going through the >> computationally expensive process of bootstrapping is not actually >> teaching me anything new, but I would like to get some sort of estimate >> of error associated with the computed p-values. Some mention has been > It looks to me as if #1 and 4 show a huge range, when > judged by the appropriate standard of relative size. > But, more important, #2 and 5 are unbelievable. > That is, I would say that they are not 'useful' results. > Either, they were not good candidates for bootstrapping, > or something is wrong that is more serious than that. They are actually what you expect, I think, from a noncentral chi-square. If sampling from a 1-df central chi-square, for example, one would expect 95% of samples to fall between 0.001 and 5.02, wth the "95% CI" for the P-values ranging from 0.05 all the way up to 0.95. By contrast, for ncp=10, say, the expected 95% range of P-values for the test of the null is 1e-6 to 0.13 (pchisq(qchisq(c(0.975,0.025),df=1,ncp=10),df=1,lower=FALSE), around a mean of 0.0016. Wrt Arlequin, it is difficult to permute around missing data (not using Windows I don't have the benefit of the updated version ;)). SNPhap imputes the missing alleles based on the surrounding haplotype for the simulation IIRC. -- | David Duffy (MBBS PhD) ,-_|\ | email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v . . ================================================================= Instructions for joining and leaving this list, remarks about the problem of INAPPROPRIATE MESSAGES, and archives are available at: . http://jse.stat.ncsu.edu/ . =================================================================
