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Topic: The same four proportional weighting factors work for each
00/01/10/11 when 0.25 is subtracted from each !!!

Replies: 506   Last Post: Nov 20, 2012 9:21 PM

 Messages: [ Previous | Next ]
 Ray Koopman Posts: 3,383 Registered: 12/7/04
Re: Finally - a result consistent with our earliest logistic
regression alignability result using a predictor derived from eS of Re

Posted: Oct 15, 2012 4:11 PM

On Oct 15, 9:40 am, djh <halitsk...@att.net> wrote:
> Here are the results of executing the (Y,Z,Y-Z) protocol on the eS
> (slope) coefficient of our regression Re = ln(c/L) on ln(c/e):
>
> 1:R1
>
> p df
>
> Y .239 2865 (at uL)
> Z .605 14342 (at uH)
> Y-Z 3.8E-10 5749 (across uL,uH)
>
> Y Z
> sum(1S-1C) -0.552 -0.243
> sum(R1S-R1C) 0.350 0.138
> diff +0.902 +0.381
> -------------------------------
>
> 2:R2
>
> p df
>
> Y .809 7724 (at uL)
> Z .308 27594 (at uH)
> Y-Z 5.5E-23 18276 (across uL,uH)
>
> Y Z
> sum(2S-2C) -0.079 -0.455
> sum(R2S-R2C) 0.098 0.273
> diff +0.177 +0.728
>
> -------------------------------
>
> 3:R3
>
> p df
>
> Y .282 936 (at uL)
> Z .074 16978 (at uH)
> Y-Z 9.0E-08 1830 (across uL,uH)
>
> Y Z
> sum(3S-3C) -0.444 -0.973
> sum(R3S-R3C) 0.390 0.350
> +0.834 +1.323
> --------------------------------

When I was a grad student, the department head, who taught one of
the Quantitative Methods courses that were required of all incoming
students, threatened to flunk any student who ever reported a table
of results that contained p-values for tests of mean differences
without giving the corresponding means. Tables such as those above
should give not only the values of Y, Z, and Y-Z, but also their
definitions in terms of the design factors. What are Y and Z ?

>
> If you look at the three lines labelled "diff", you'll see immediately
> why we got weaker and more inconsistent results than desired when we
> attempted to predict structural alignability using a predictor derived
> from the eS coefficient of Re for the dicodon subset 1S. (If you go
> back in the s.s.m "archive" here, you'll see that we really only got
> believable results for just the one fold a1 using a predictor derived
> from the eS coefficient of Re for the dicodon subset 1S and u-level =
> uA (all).)
>
> In particular, the three "diff" lines together imply that we will get
> our biggest bang for the buck if we use predictors derived from the eS
> coefficients from runs on the dicodon subset 2S or 3S with u-level set
> to uH, NOT the dicodon subset 1S.
>
> Also, the sum and diff lines for Z for 2:R2 and 3:R3 accord precisely
> with the fundamental energetic hypothesis we've been pursuing. This
> is because these lines indicate that:
>
> a) for non-randomly constructed uH (i.e. Z) data, the eS coefficient
> of Re is essentially negative
>
> b) for randomly constructed uH (i.e. Z) data, the eS coefficient of Re
> is essentially positive.
>
> And this is exactly as expected: the representation level (ln(c/L) of
> our dipeptides of interest correlates NEGATIVELY with the energetic
> level (ln(c/e) of the dicodons underlying these dipeptides.
>
> Why? Because the underlying O-F index was constructed so that
> energetic favorability INCREASES as the index value DECREASES.
>
> ASSUMING that the above analysis is defensible, it bodes well for our
> increased success in structural alignability prediction for two main
> reasons:
>
> a) we can now use two sets of predictors derived BOTH from the eS
> coefficients of Re for(2S,uH) AND from the eS coefficients of Re for
> (3S,uH) data, rather than just a predictor derived from one set of
> data;
>
> b) we can actually look at the underlying sequences and find those
> that belong to the INTERSECTION of the (2S,uH) data and the (3S,uH)
> data, and then compare alignability results on these most "highly-
> valued" sequences vs other "less-valued" sequences.
>
> But note the "ASSUMING" in the above paragraph - I realize that you
> may well conclude that:
>
> c) the tables for eS exhibited above do not support ANY meaningful
> conclusions about the role of energetics in dipeptide over-
> representation;
>
> d) or, entirely different conclusions than the ones I've drawn above.
>
> Thanks as always for the time you'll spend considering the above. In
> the meantime, I'll be doing the (Y,Z,Y-Z) analysis on the remaining
> six coefficients.

Date Subject Author
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