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st: haplologit-genetic association


From   Jane Maguire <Jane.Maguire@newcastle.edu.au>
To   statalist@hsphsun2.harvard.edu
Subject   st: haplologit-genetic association
Date   Wed, 26 Aug 2009 14:39:27 +1000

Dear all
Data is case control, snps are coded 0,1,2 
One gene, two snps. Haplotype for hap00 is quite rare and when interaction term (cox2use) is added the output is rubbish. I am not a biostatistician- am a Phd student in medicine and Public Health. However, I think the problem is the numbers are too small...unless I have made a coding error? any advice?

This command works- without interaction,

xi: haplologit stroke i.cox2use i.aspirin i.nsaid i.gender i.agegroup2 i.bmigroup2 i.Diabetes4 i.HT i.AF2 ///
 (i.Smoker) if ~(inlist(kozak,.) & inlist(thrmet,.)), snpvars(kozak thrmet) inher(d) ///
                   riskhap1("11") ///
					 happrefix(_hap) or noemtable noemshow

But this one doesn't,

set more off
xi: haplologit stroke i.cox2use i.aspirin i.nsaid i.gender i.agegroup2 i.bmigroup2 i.Diabetes4 i.HT i.AF2 ///
 (i.Smoker) if ~(inlist(kozak,.) & inlist(thrmet,.)), snpvars(kozak thrmet)  ///
                   riskhap1("11", inter(cox2use))  ///
					inher(d) happrefix(_hap) or 

Many Thanks
Jane

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