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
