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Topic: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Replies: 148   Last Post: May 8, 2012 3:40 AM

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Ray Koopman

Posts: 3,382
Registered: 12/7/04
Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Posted: Apr 7, 2012 2:07 AM
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On Apr 6, 8:09 pm, djh <halitsk...@att.net> wrote:
> Below are two sets of results from John's calculator.
>
> The first set you've seen before - they're the "length 20" results
> using the two predictors (v1+v)/2 and v1-v2.
>
> The second set of results is also based on a matrix for length 20
> using the same two predictors.
>
> The difference is that in this case, I used only data exhibiting a
> value of 3 for the new "C" variable which I mentioned in my last post,
> rather than allowing C to be any of the values 2 thru 6 which it
> actually assumes in the length 20 data. (In other words, I have not
> yet incorporated "C" into the model as a third predictor - right now I
> am merely using the original two predictors but on data in which C is
> constant - just to see what happens.)
>
> As you can see from the two sets of results:
>
> a) the chi-square drops from 483.0906 in the first set of results to
> 12.6410 in the second set, roughly a 40-fold decrease;
> b) the p-value associated with the chi-square goes from < 0.0001 to
> 0.0018.
>
> Does this drop in chi-square signify a step in the right direction, or
> is 12.6410 still a relatively "big" chi-square? We would of course
> like you to say that this drop in chi-square is a step in the right
> direction, because we can think of "C" as a scalar on our unquantized
> variable u that underlies v.
>
> Thanks for any time you can afford to spend considering this question,
> and again, please forgive my abysmal ignorance about these matters.


This is just a quick note to sort out the chi-squares.
I'll have more to say later.

The chi-square I described in my previous post compares the logistic
model to the saturated model, that fits the data perfectly.
The bigger the chi-square (and the smaller the p), the more certain
you are that the logistic model is worse than the saturated model.

The chi-square in John's output compares the logistic model to the
"null" model, that gives all the cells the same probability.
The bigger the chi-square (and the smaller the p), the more certain
you are that the logistic model is better than the null model.

So you want my chi-square to be small and nonsignificant,
and John's to be big and significant.

For another take on how well the model fits, plot the "Calc Prob"
in John's output as a function of the sample proportion, n1/(n0+n1).
Ideally, the two should be equal.
How far is the plot from a 45 degree line?


Date Subject Author
4/1/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/3/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/3/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/6/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/6/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/6/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/7/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/7/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/8/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/8/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/9/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/9/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/9/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/9/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/9/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/10/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/10/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Art Kendall
4/11/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/13/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/13/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/13/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/15/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/15/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/15/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/15/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/17/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/17/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/17/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/18/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/19/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/19/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
gimpeltf@hotmail.com
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
gimpeltf@hotmail.com
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
gimpeltf@hotmail.com
4/21/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
gimpeltf@hotmail.com
4/21/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/24/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/22/12
Read Our first control group result is precisely how we want AML's program
to behave with control group data ....
Halitsky
4/23/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/24/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/24/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/24/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/24/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/26/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/26/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/26/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/27/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/27/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/27/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
gimpeltf@hotmail.com
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
gimpeltf@hotmail.com
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/29/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/29/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/29/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/29/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/29/12
Read Your questions go to the "moment of truth" that Jacques and Arthur
may shortly be facing
Halitsky
4/29/12
Read Re: Your questions go to the "moment of truth" that Jacques and
Arthur may shortly be facing
Halitsky
4/29/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/30/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
5/1/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
5/1/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
5/1/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
5/1/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
5/1/12
Read Results for c1 study and control groups when model run WITHOUT the
four cells for shortest length interval 33-42
Halitsky
5/2/12
Read Results on c2 fold confirm peculiarity of length interval 33-42 seen
in c1 fold results
Halitsky
5/2/12
Read Model with adjusted weighting logic now works on c2 fold! (but PLEASE
review my new weighting logic !)
Halitsky
5/2/12
Read Actually, your original suggestion (input counts) works as well as
what I just posted for the c2 fold
Halitsky
5/3/12
Read Re: Actually, your original suggestion (input counts) works as well
as what I just posted for the c2 fold
Ray Koopman
5/3/12
Read Re: Actually, your original suggestion (input counts) works as well
as what I just posted for the c2 fold
Halitsky
5/3/12
Read Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}
Halitsky
5/4/12
Read Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}
Ray Koopman
5/4/12
Read Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}
Halitsky
5/4/12
Read Your question re significance of proportion involving counts of
01:10:01:11 inputs to Arthur's program
Halitsky
5/4/12
Read Results of both chi-square tests on all six folds
Halitsky
5/4/12
Read Re: Comparative results for {lnL,w,lnLw,x1,x2} & {lnL,w,lnLw,x1,x2,lnLx1,lnLx2}
Halitsky
5/4/12
Read I'm sending the a1 CI table off-line, since the format didn't hold here.
Halitsky
5/5/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Halitsky
5/5/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Ray Koopman
5/5/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Halitsky
5/7/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Halitsky
5/7/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Halitsky
5/8/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Ray Koopman
5/8/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Halitsky
5/6/12
Read Re: I'm sending the a1 CI table off-line, since the format didn't
hold here.
Ray Koopman
5/3/12
Read Could I ask you to check this 1st test using sum of chi-squares from
study vs control cells ?
Halitsky
5/3/12
Read Re: Could I ask you to check this 1st test using sum of chi-squares
from study vs control cells ?
Ray Koopman
5/3/12
Read Re: Could I ask you to check this 1st test using sum of chi-squares
from study vs control cells ?
Halitsky
5/3/12
Read Could I ask you to check this 1st test using converged likelihoods
for study/control/pooled runs?
Halitsky
5/3/12
Read Re: Could I ask you to check this 1st test using converged
likelihoods for study/control/pooled runs?
Ray Koopman
5/3/12
Read Re: Could I ask you to check this 1st test using converged
likelihoods for study/control/pooled runs?
Halitsky
5/1/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/27/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Ray Koopman
4/28/12
Read Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....
Halitsky
4/24/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/19/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/20/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/16/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/14/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman
4/13/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Halitsky
4/8/12
Read Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs
Ray Koopman

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