David Duffy wrote: > > What kind of bootstrap have you used? And how many genotypes in the > observed data? You might remember that bootstraps can be parametric or > nonparametric, and that in the latter case, various types of bias > correction need to be applied when producing CIs. Also, the variation > in P-value for each bootstrap sample reflects both the size of the > original sample and the number of permutations used. You might compare > your LD P-values to the (Fisher) exact P-values for the genotypic > contingency table (if there is HWE and no intergametic association, > these shouldn't be too different, and do give a "trustable" upper > bound). Of course, you can also compare to results from Arlequin, > multiple replicates from SNPhap etc for the same data.
All due respect to the makers of Arlequin, but I don't have a lot of faith in their software. Unless they've fixed it, they treat unknown alleles as new alleles in LD computations, which is worrying. Enda Kelly --------------------------------------------------------------------- E-mail Confidentiality Notice and Disclaimer This email and any files transmitted with it are confidential and are intended solely for the use of the individual or entity to which they are addressed. Access to this e-mail by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is prohibited. E-mail messages are not necessarily secure. Hitachi does not accept responsibility for any changes made to this message after it was sent. Please note that Hitachi checks outgoing e-mail messages for the presence of computer viruses. --------------------------------------------------------------------- . . ================================================================= Instructions for joining and leaving this list, remarks about the problem of INAPPROPRIATE MESSAGES, and archives are available at: . http://jse.stat.ncsu.edu/ . =================================================================
