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Re: st: haplologit-genetic association


From   Neil Shephard <nshephard@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: haplologit-genetic association
Date   Wed, 26 Aug 2009 08:47:58 +0100

On Wed, Aug 26, 2009 at 5:39 AM, Jane
Maguire<Jane.Maguire@newcastle.edu.au> wrote:
> 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.

What does "rubbish" mean?

> I am not a biostatistician- am a Phd student in medicine and Public Health.

You'd benefit from getting your head round the basics of statistics in
the long run.  A good book is Intuitive Biostatistics by Harvey
Motulsky.  Not too heavy on the maths, but explains things very well.

> 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

As per above, what does "rubbish" mean?  If you could show the output
of running these two commands it would be more informative for those
on the list who might then be able to comment on what the problem is.

Neil


-- 
"The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data." ~ John Tukey (1986), "Sunset salvo". The American
Statistician 40(1).

Email - nshephard@gmail.com
Website - http://slack.ser.man.ac.uk/
Photos - http://www.flickr.com/photos/slackline/

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