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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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gimpeltf@hotmail.com

Posts: 13
Registered: 4/20/12
Re: Our first control group result is precisely how we want AML's
program to behave with control group data ....

Posted: Apr 28, 2012 7:33 PM
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You wrote:

> I thought m1 was x1*x2 and had values 0,0,0,1. In any case,
> how do the four cells of the 2x2 design map into 0,1,2,3 ?
> Or is it something completely different?



Yes - you're correct m1 is 0,0,0,1 ... I was thinking of x1 = 0 0 1 1
when I typed that.

In any event, 0,1,2,3 are just a better way of "gradating" the pairs
of residuals we obtain from our two regressions:

lnc-lne on lnc-lnL (call this regression Re)
lnc-lnu on lnc-lnL (call this regression Ru)

For the new variable mv:

0 means residual above the median for both Re and Ru (like x1 = 0
x2 = 0)
1 means residual above the median for Re but below for Ru (like x1 = 0
x2 = 1)
2 means residual below the median for Re but above for Ru (like x1 = 1
x2 = 0)
3 means residual below the median for both Re and Ru (like x1 = 1
x2 = 1)

The idea here is that a residual below the median for Ru is better
than one above the median for Ru, but doesn't count "as much" as a
residual below the mean for Re.

You wrote:

"Yes, but (as I've said before) you still should test the difference
between the coefficients. Only if both coefficients are individually
significant and they have different signs can you skip testing the
difference.

Call the coefficients b1 & b2, and their standard errors s1 & s2.
Get z = (b1 - b2)/sqrt[s1^2 + s2^2], and refer it to the standard
normal distribution (as I described in my 10:48 am post earlier
today). "

I will do this for two reasons: i) because you've told me to; ii) I
want to learn how to do it.

But I want to wait to do this until after I've run the new model
{lnL,mv,lnLmv} against the remaining five folds. I want to see first
if the pattern holds up of the confidence intervals for mv and lnLmv
staying on either side of 1 for the study group, but crossing 1 for
the control group.

In this regard, I've run the new {lnL,mv,lnLmv} model against the a3
study and control groups and the pattern DOES hold up:

a3 Study Group:

14376 cases have Y=0; 1176 cases have Y=1.

Overall Model Fit...
Chi Square= 437.7746; df=3; p= 0.0000

Coefficients and Standard Errors...
Variable Coeff. StdErr p
1 4.2503 0.3094 0.0000
2 1.4813 0.6778 0.0289
3 -0.4283 0.1741 0.0139
Intercept -18.6238

Odds Ratios and 95% Confidence Intervals...
Variable O.R. Low -- High
1 70.1255 38.2413 128.5933
2 4.3988 1.1650 16.6082
3 0.6516 0.4632 0.9165

a3 Control Group:

466 cases have Y=0; 27 cases have Y=1.

Overall Model Fit...
Chi Square= 23.6075; df=3; p= 0.0000

Coefficients and Standard Errors...
Variable Coeff. StdErr p
1 1.9369 2.3111 0.4020
2 -6.9445 5.2765 0.1881
3 1.8649 1.3539 0.1684
Intercept -10.4753

Odds Ratios and 95% Confidence Intervals...
Variable O.R. Low -- High
1 6.9370 0.0748 643.2717
2 0.0010 0.0000 29.8908
3 6.4554 0.4544 91.6990

And I will post the results for b1 later tonight, but I'm pretty sure
these will maintain the pattern, because b1 worked so well even with
your original model (i.e. chi-squares relativized to sample size were
something like .29 and .16 for study and control group.)



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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