On Dec 2, 9:28 am, djh <halitsk...@att.net> wrote: > You wrote: > > ?Or maybe analyze at each individual length (interval-width = 1)?? > > As you pointed out early on in this effort, danger inheres in > ?cleaving nature? by ANY choice of length interval when the empirical > situation is still murky (even though some cleavages can be more/less > defensible than others on purely technical grounds.) > But in our case I think a special danger lurks in ANY length interval > cleavage we make because even though we haven?t studied how long > important structural subunits actually are in different folds (length > = number of amino acids = number of codons), our length interval > cleavages (equi-width OR equi-ratio) not only imply that we do have > this privileged knowledge, but also imply that any u,e-based > ?profiles? relevant to evolution of important structural subunits > should be defined on a particular set of length intervals rather than > another. > > So in the case of some folds, we might get lucky with our choice of > length intervals (as the good Aug two-ways for certain length > intervals within folds a1,b1,c1,c2 seem to indicate), while with other > folds such as a3 and b47, our luck may not hold up (as the absence of > any good Auq two-ways for any length intervals within folds a3 and b47 > seems to indicate. > > And the only way to stop playing this kind of russian roulette with > the data is to take your suggestion and drop back to singleton length > intervals. > > This will, of course, lead to some Bonferroni issues later on > because given the fact that our singleton lengths range roughly from > 25 to 125,
25 to 125 ? My records show 24 to 124. (There was a problem a while ago with lengths being off by 1, but I thought it was fixed.) In any case, is there a big table -- 6 x 3 x 2 x 2 x 101 -- of the Ns at each length in each (fold,set,subset,moss) cell? (If I already have the data that will let me get the Ns myself, I've lost track of it. Do you remember when you sent it and/or what file names you used?)
> we?ve multiplied Bonferroni entries by a factor of 8.5 (= > 100/12). But it is to be hoped that if the move to singletons is > correct, the data will show us natural groupings for Bonferroni > tables that we can?t see now. > > Anyway, I?ve completed the code additions for the second new > regression, and desk-checked them. > > So now I?ll rerun the analysis for the first and second regressions > using singleton length intervals and post back when complete. > > Thanks again for your continued consideration of these matters, and > please feel free to again interject ?unilaterally? if any other > changes occur to you that might increase our chances of success, or > at least decrease our chances of arrogant methodological error.