# RE: st: Processing speed for ttest

 From "Wallace, John" <[email protected]> To [email protected] Subject RE: st: Processing speed for ttest Date Thu, 9 Oct 2003 11:42:51 -0700

```Thanks very much, David.  I adapted the code you supplied and it worked
amazingly well.  I had my 3 sets of t values in 12 seconds.  The Holland
method is shown as an "improved sequentially rejective Bonferroni test
procedure" in the abstract listing from the smileplot help.  I'm familiar
with the Bonferroni correction, but is there a nutshell explanation for what
the Holland method is doing in establishing a significance threshold?

Thanks also to Nick Winter, Nick Cox, and William Gould for the original
ttest speed discussion and resulting code.  I'm awash in vast seas of raw
data at the moment, and efficient statistics are becoming more important
with each passing day (and microarray version).

-----Original Message-----
From: David Airey [mailto:[email protected]]
Sent: Wednesday, October 08, 2003 10:22 PM
To: [email protected]
Cc: Wallace, John
Subject: re: st: Processing speed for ttest

John,

See the threads started by me on

Subject: st: give me some speed
Date: Thu, 4 Apr 2002 14:07:38 -0600

on analysis of Affy chip data by ttests and the many helpful responses.
You have to use the Harvard archives to find this and related threads.
There is a way to make the ttests very, very fast (2 seconds for 12K
ttests), pointed out by Nick Winter, the winner of the speed contest.
But your intuition to use an alternative form of the ttest (regress)
will get you a quicker result too, as William Gould detailed.

clear
set more off
insheet using cxb.txt

/*
f1 f2 f3 f4 f5 f6 c1 c2 c3 c4 c5 c6 <--wide format, forebrain and
cerebellum results for animals 1 to 6.
*/

display "\$S_TIME"

forvalues j = 1/6 {
generate d`j' = f`j'-c`j'
}

egen dif_mean = rmean(d1-d6)
egen dif_sd = rsd(d1-d6)
egen dif_n = robs(d1-d6)
generate t = dif_mean/(dif_sd/sqrt(dif_n))
generate tp = tprob(dif_n-1,t)

display "\$S_TIME"

save Winter, replace

smileplot, pvalue(tp) estimate(t) method(holland) nhcred(retain)
list t tp if retain == 0
set more on

*this takes 2 seconds for all 12422 ttests or 0.016 seconds per 100
ttests
*
*   For searches and help try:
*   http://www.stata.com/support/faqs/res/findit.html
*   http://www.stata.com/support/statalist/faq
*   http://www.ats.ucla.edu/stat/stata/
```