From: Leitch, Matthew C.
Sent: Monday, January 24, 2011 6:53 PM
To: 'i...@network-theory.co.uk'
Subject: question about the pt() calculation
Hello
Thank you for your time. I am a graduate student at the University of Texas
Medical Branch, and I was wondering if you could help me with a R program I am
writing. I have some data that is stored a file that has 1733 rows and 4
columns. Each row is independent, so I have a loop system so I don't have to
manually perform 1733 t-tests. However I got most of it to work, thanks to the
"An Introduction to R" book and a helpful colleague. But I am having some
difficulty with getting my t-test scores converted to p-values. The pt() test
won't take the t object, but I am unsure how to make it create a p-value for
each row. If you have any suggestions they would be greatly appreciated.
Best Wishes
Matt
cancer<-read.table("group2.txt", header=TRUE)
noncancer<-read.table("group1.txt", header=TRUE)
#meanc<-mean(cancer)
#meannc<-mean(noncancer)
#varc<-var(cancer)
#varnc<-var(noncancer)
#Sx1x2<-sqrt((varc+varnc)/2)
#n<-4
#t<-(noncancer-cancer)/(Sx1x2*(sqrt(2/n)))
#df<-(2*n)-2
#pt(t,df)*2
answer = matrix(,1733,1);
alpha = 0.05;
#for(i=1:1733)
#{
# meanc = mean(cancer[i,]);
# meannc = mean(noncancer[i,]);
#
# varc = var(cancer[i,]);
# varnc = var(noncancer[i,]);
#
# Sx1x2 = sqrt((varc+varnc)/2);
# n = 4;
# t = (noncancer-cancer)/(Sx1x2*(sqrt(2/n)));
# df = 2*n - 2;
#
#
# answer[i,1] = pt(t,df)*2;
#
# if (answer[i,1] = alpha)
# {
# sing.
# }
# else
# {
# nonsing.
# }
#}
for(i in 1:1733)
{
meanc = mean(cancer[i,]);
meannc = mean(noncancer[i,]);
varc = var(cancer[i,]);
varnc = var(noncancer[i,]);
Sx1x2 = sqrt((varc+varnc)/2);
n = 4;
t = (noncancer-cancer)/(Sx1x2*(sqrt(2/n)));
df = 2*n - 2;
answer[i,1] = pt(t,df)*2 ;
if (answer[i,1] < alpha)
{
banswer[i,1] = 1;
}
else
{
banswer[i,1] = 0;
}
#ifelse(answer[i,1] < alpha, banswer[i,1] = 1, banswer[i,1] = 0);
}______________________________________________
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