*shrug* i thought i was used to LINKAGE, but...
(1) i posted a note to this group a few days ago [thanks to those who
responded] about bizarre MLINK results, namely "-infinity" results in
some families. well, now i get some more bizarre results, but ones
that aren't as obvious to spot... take this example of a disease v.
marker 2-pt MLINK lod score :-
theta lod
0% 0.003
1% 0.002
5% -3.079
10% -3.045
20% -2.something
etc etc
(i am making the figures up from memory, so don't quote me, but
they are roughly what happened)
soooooo, what gives ? is this just a variation on the problem i posted
about a coupla days ago, or not ? also is there any valid reason for
this sort of lod-score curve. i don't think so. this is beginnging
to get annoying. -infinities (grammer?!) are easy to spot, but if
i'm doing a 350-marker genome scan, as i am, i could easily miss this
sort of crap. oh dear, woe is me.
(2) ILINK. this is fun. i am using ILINK to try and estimate allele
frequencies for loads of markers. i know that i am using a 14-allele
system, so i code my DATAIN.DAT file for 14 alleles at 1/14 equal
starting values. i tell ILINK to do the sums, but is stops after
1 iteration, and gives up. i see that my PEDIN.DAT file has no
allele 14. i play about, and find that if i do not have a "n" allele
in my PEDIN.DAT file, then ILINK stops, but if i change one person
from a 2-12 to a 2-14, then ILINK works luvverly, and gives me proper
frequency estimates. why ? there are no individuals in my PEDIN.DAT
file with either a 2 or a 7 or a 11 allele, but ILINK doesn't complain.
am i missing something stupid ? is ILINK stupid ? i've run a few tests,
and it always craps out early if there is no "n" allele for an "n"-allele
system. oh dear, woe is me.
for both (1) and (2) i am using version 5.2 of LINKAGE on the pc. i am
using a dos-pc, and will start using a lot of alcohol if i can't get
these problems fixed. hhhhheeeeeeellllllllppppppp !!
Iain "Help" Fenton, Cardiff, UK.
