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Re: st: Ologit storing p-values up to 10 decimal places


From   Debs Majumdar <debs_stata@yahoo.com>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   Re: st: Ologit storing p-values up to 10 decimal places
Date   Mon, 8 Aug 2011 11:55:03 -0700 (PDT)

Thanks Nick. I was just trying to do a Genome Wide Association test with a trial sample of 500 SNPs. In a normal dataset, we have around 500,000 SNPs and the p-values are very small (the last one I ran in PLINK had the top hit at 5e-17). I would eventually want to modify the code so that it runs fo 500K SNPs. The reason for trying to run the GWAS in Stata and not PLINK is that PLINK doesn't have the capability of doingan ordinal logistic regression.


  I got confused with the code. Sorry for that. If I wanted to print out the sorted p-values would adding an extra line (sort e(p)) do it?  


Also, I just noticed that Stata 11 has a  --pformat-- option. I was wondering if that can be used before the loop to specify that I want p-values upto certain decimal places.


Thanks,

 Debs



foreach var of var length-gratio {
    capture ologit rep78 `var'
* sort p-values
  sort e(p)

    di "`var' {col 20}" %12.10f e(p)
}


----- Original Message -----
From: Nick Cox <njcoxstata@gmail.com>
To: statalist@hsphsun2.harvard.edu
Cc: 
Sent: Monday, August 8, 2011 11:19 AM
Subject: Re: st: Ologit storing p-values up to 10 decimal places

Your code is very confused, mixing up macros and variables and
assuming that values exist which you never assigned. However, with the
big caveat that no P-value can be trusted out to the tenth decimal
place, the technique in this may be a start at what you seek.

webuse fullauto

foreach var of var length-gratio {
    capture ologit rep78 `var'
    di "`var' {col 20}" %12.10f e(p)
}

For more manipulation, look at -postfile-.

If you are inspecting that many P-values, also consider building in a
penalty for chance hits.

On Mon, Aug 8, 2011 at 6:59 PM, Debs Majumdar <debs_stata@yahoo.com> wrote:

>    I am trying to write a code which will go through around 500 ordinal logistic regressions and the output is the id for each of the rs # and the corresponding p-values, where the p-values are sorted in ascending order. i want the p-values reported up to 10 decimal places. This is my code so far. I may be wrong here. How do I make Stata report p-values up to 10 decimal places? Do I need to specify e(b) under display if I want the beta coefficients printed out for each rs #?
>
>
> ~~~~~~~~
> local list "age sex c1 c2 c3"
> local pvalue = e(p)
>
> foreach `x’ of varlist rs1-rs500 {
>
> quietly ologit outcome `x' `list'
>
> sort pvalue
> display `x' pvalue
> }
>
> ~~~~~~~~
>
> I am using Stata 11.1.
>
> I want the output to show the following:
>
> ~~~~
>
> rs5       5e-7
> rs493   4e-6
> ...
> ...
> rs257   0.33
>
> ~~~

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