Rich Ulrich <[EMAIL PROTECTED]> wrote: > On 21 Oct 2003 05:44:47 GMT, David Duffy <[EMAIL PROTECTED]> > wrote:
>> Rich Ulrich <[EMAIL PROTECTED]> wrote: > [ ... ] >> > On 17 Oct 2003 06:05:19 -0700, [EMAIL PROTECTED] (Enda Kelly) > [ editing and rearranging the table ] >> >> Locus pair P-value Median Lower Upper >> >> 1 0.002414 0.002422 0.000055 0.037401 >> >> 4 0.018936 0.016100 0.001082 0.193285 >> >> 2 0.971621 0.512296 0.181935 0.850761 >> >> 5 0.832001 0.505662 0.173286 0.857703 > [ ... ] > DD > >> 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 > David, you mis-read, I hope. I can see that your > description fits what I said about #1 and #4. Yes, > I was not surprised by the wide, multiplicative range > of the p-levels. The original poster called those *narrow* > since the whole action was within a percentage point; > I objected. > It was just the #2 and #5 that were not 'useful' results, > since the point estimate is outside the CI, for #2, and > nearly so for #5. That can happen, but it is pathological. > Agreed? Surely. I would guess that in #2 and #5, the table is sparse, so that the "observed" P-value hinges on one cell of size 1-2. I am always surprised by how much the (Fisher) P-value moves around when one combines cells of small size (plus people complain when their publishable P-value disappears ;)). And I'm personally still not sure how to interpret such results, specifically when looking at association with a rare risk factor/haplotype, given that adding just a few more observations to a study can make a fair difference. The problem, in this particular domain, is that there can be many rare haplotypes, some of which merely represent measurement (genotyping) errors. . . ================================================================= Instructions for joining and leaving this list, remarks about the problem of INAPPROPRIATE MESSAGES, and archives are available at: . http://jse.stat.ncsu.edu/ . =================================================================
