Date: Dec 2, 2012 1:35 PM
Author: Ray Koopman
Subject: Re: Glad you brought up “singleton” length inter<br>	vals ... been thinkin’ on ‘em also ...

On Dec 2, 9:28 am, djh <> 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.