In article <1994Sep29.073020.20826 at news.unige.ch> mike at divsun.unige.ch (Mike Morris) writes:
> What is a generalized lod score? How is it calculated? Why is it higher
>than my better marker?
>The generalized lod score is
log10( L( theta1, theta2)/ L(theta1=0.50, theta2 = 0.50) )
where theta1 and theta2 are the two recombination fractions.
Dr. Jurg Ott's book describes the generalized lod score as
a measure of "the overall evidence that a set of loci form
a linkage group."
The generalized lod score is not relevant to what you
would like to compute. To compute a multipoint lod
score with the distance between the markers fixed,
use linkmap instead of ilink. Note that a multipoint
lod score may be higher than either of your pairwise
lod scores, since markers that are uninformative in
the pairwise analyses may be jointly informative in
the multipoint analysis.
Sincerely,
-- Dan Weeks --
