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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: Do you have any suggestions about how to "convert" the O-F index
for our purposes?

Posted: Oct 22, 2012 2:15 PM

On Oct 22, 3:49 am, djh <halitsk...@att.net> wrote:
> [Explanatory note to Jacques/Arthur/Marvin: the "e" that Ray is
> talking about here is an average O-F value computed from the O-F
> values of the individual base-pair doublets in a set of one or more
> codons, the way we always have.]
>
> You wrote:

> > As usual, I'm still several steps behind you. I'm worried about e.
> > It may be on a 0...max scale that is easily interpretable and that
> > relates (approximately, on average) linearly to temperature, but that
> > doesn't mean that it's legitimate to use e in a ratio or take its log
> > -- both of which are things that should not be done with Celsius or
> > Fahrenteit temps, but can be done with Kelvins. In other words, I
> > fear the zero on the e scale is a Celsius zero, not a Kelvin zero.

>
> If I were not completely automated at this point, I would of course be
> concerned with the time it would take to re-run the entire analysis
> using a new definition of our "e" based on an O-F index that has
> somehow been converted to avoid the problem you note above.
>
> But since a complete re-run is now only a matter of a day and a half,
> my concern is solely theoretical.
>
> Namely, is it possible to "convert" the O-F scale so as to give us a
> defensible basis for our computation of "e" as an average across a set
> of dicodons?

It can probably be done, but I still don't understand e completely.
All the individual values are in [0, 2.86]. If they are averaged and
then divided by the maximum possible (i.e., 2.86), how do values > 1
arise?

>
> Please let me know your thinking here and I will of course pass on
> your thoughts to Jacques and Arthur.
>
> Thanks as always.

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