LOD score too high - answers

Daniel E. Weeks dweeks at WATSON.HGEN.PITT.EDU
Fri Feb 10 09:59:52 EST 1995


On 9 Feb 1995, Daniel E. Weeks wrote:
> > To test the hypothesis of all linked against none 
> > linked you'd have 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.5 - 3, which 
> > would mean changing two intervals simultaneously. 
> 
>    Unfortunately, this is exactly what LINKMAP does when it computes 
> Ott's generalized lod score (which is described in his book).  

  Opps, it is ILINK which computes Ott's generalized lod score, not MLINK or
LINKMAP.  David Curtis' discussion of MLINK was correct - MLINK does only
change one theta at a time, and, as pointed out, this may result in a 'lod
score' that is not a proper multipoint lod score because it was standardized
by the wrong likelihood. 

-- Dan Weeks --



More information about the Gen-link mailing list