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.