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Re: st: permutations
.
Do you have access to the manual help or online help? The syntax is:
permute permvar exp_list [, options] : command
You specified permvar but not exp_list, so I'm not sure what permute
is defaulting to, maybe just the overall model statistic? You can
write a small program to return the coefficients for the genetic dummy
variables, and an overall test of those, that gets called by permute.
The ANOVA example in the printed help shows how to do this.
T is your statistic
T(obs) is your observed statistic
c is the number of times the statistics is greater than T(obs)
n is the default number of permutations since you didn't specify this
either
Below is an example from ATS UCLA (Stata version 9/10):
* read your data into Stata
use http://www.ats.ucla.edu/stat/stata/notes/hsb2, clear
generate goodread = (read > 60)
* run logistic predicting "goodread" from "write"
logit goodread female
* run permutation test for above with 10000 repetitions
permute female x2=e(chi2), reps(10000) nodots: logit goodread female
Since you want a statistic for the individual dummy variables and the
test for both genetic dummy variables, you don't just want the results
from the overall test, and you cannot just collect that using permute
as the above example does.
-Dave
On Mar 13, 2008, at 4:46 AM, Christopher Intemann wrote:
Hi,
I just realized that stata is capable of doing permutations.
However, I find it quite difficult to figure out how:-)
Within the scope of a genetic analysis I'm using a command like:
xi:logistic affected_stata i.gene age ethno_x sex_x
where gene is coded as 1/2/3, referring to genotypes AA/AG/GG (for
instance).
The result is corrected for confounders age, ehtnicy and sex.
I played around a bit. I was trying this command line:
permute affected_stata "xi:logistic affected_stata i.MCP1_7656en age
ethno_x sex_x" e(chi2)
and I got a result which is probably wrong (or at least I don't
understand it):
Monte Carlo permutation statistics Number of obs
= 4356
Replications
= 100
------------------------------------------------------------------------------
T | T(obs) c n p=c/n SE(p) [95% Conf.
Interval]
-------------
+----------------------------------------------------------------
_pm_1 | 76.09804 0 100 0.0000 0.0000
0 .0362167
------------------------------------------------------------------------------
Well. Any help would be appreciated:-)
Many thanks in advance,
Chris
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