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analysis question

Dmitri Zaykin zaykin at statgen.ncsu.edu
Thu Feb 6 17:13:56 EST 1997

smallm at PBS.DFO.CA wrote:
> I am in the process of analyzing some microsatellite population data
> and have come up with some puzzling results.  At one locus a few of
> my populations came up as out of Hardy-Weinberg equilibrium with a 
> p value of 0.000 using GENEPOP. I compared results with CHIHW and these
> populations were now in Hardy-Weinberg equilibrium with p values ranging
> from 1.0 to 0.96.

Hmm.. Since it is me who wrote CHIHW, I'd be probably the best 
person to answer questions about it :) 

Does the version that you have distinguishes between upper- and 
lower case in the input file?

> I tested CHIHW with a population that I knew was out of equilibrium
> since it had a null allele present at 60%, 30 observed heterozygotes
> and 130 expected heterozygotes.  CHIHW indicated the population was
> also in equilibrium with a p value of 0.96 yet the Selinger's D value
> (the probability that the observed heterozygosity equals expected
> heterozygosity) was 0.000.  GENEPOP uses a Markov chain randomization and
> CHIHW uses a Monte Carlo procedure so I would not expect such differences
> between results. Has anyone compare CHIHW with other programs and gotten
> contrasting results? or can anyone explain how these results are possible?

I doubt there are any hideous bugs in my code. I suspect there is
something wrong with the data file. If you email it to me, I'll look
at it. 

>	Thank you, Maureen Small


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