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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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Halitsky

Posts: 600
Registered: 2/3/09
Re: Correct way to normalize an rmsd-based distance metric used in
repeated trials of pairs

Posted: Apr 15, 2012 11:24 AM
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Thanks, Ray.

I understand everything you wrote, but am not sure of the "bottom-
line".

Are you saying that if I can't got homoscedasticity by taking logs or
some other means, then I have to throw out all the c/e on c/L and c/u
on C/L correlations as essentially meaningless?

Or are you saying that I CAN use these the residuals of these
correlations to get binary logistic predictors (via median-based
dichotomization as per your suggestion), but that the chance of this
approach working is considerably lessened by the fact the residuals
are not homoscedastic?

While awaiting your response, I will start taking logs and see what
happens.



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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