I use the lcp program with MLINK to do my linkage analysis.
The first locus is the disease (2 alleles: affected or not) and the next
ones are microsatellite markers.
Preplink does not seem to calculate the allele frequencies of each
marker (according to the data I've entered with the makeped program ie
family member, status, alleles for each marker...) and gives by default
2 alleles with 0.05 of frequency for each one (that's wrong!).
What do i have to do to to have the right allele frequencies calculated
according to my results?
thanks very much for your help.
Laurence
