[R] help in interpreting paired t-test

[Greg Snow]

It looks like Bland-Altman procedures would be appropriate for this project (http://en.wikipedia.org/wiki/Bland-Altman_plot).  

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Pedro Mardones
Sent: Tuesday, September 20, 2011 11:47 AM
To: R-help at r-project.org
Subject: [R] help in interpreting paired t-test

Dear all;

A very basic question. I have the following data:

************************************************************************************

A <- 1/1000*c(347,328,129,122,18,57,105,188,57,257,53,108,336,163,
62,112,334,249,45,244,211,175,174,26,375,346,153,32,
89,32,358,202,123,131,88,36,30,67,96,135,219,122,
89,117,86,169,179,54,48,40,54,568,664,277,91,290,
116,80,107,401,225,517,90,133,36,50,174,103,192,150,
225,29,80,199,55,258,97,109,137,90,236,109,204,160,
95,54,50,78,98,141,508,144,434,100,37,22,304,175,
72,71,111,60,212,73,50,92,70,148,28,63,46,85,
111,67,234,65,92,59,118,202,21,17,95,86,296,45,
139,32,21,70,185,172,151,129,42,14,13,75,303,119,
128,106,224,241,112,395,78,89,247,122,212,61,165,30,
65,261,415,159,316,182,141,184,124,223,39,141,103,149,
104,71,259,86,85,214,96,246,306,11,129)

B <- 1/1000*c(351,313,130,119,17,50,105,181,58,255,51,98,335,162,
60,108,325,240,44,242,208,168,170,27,356,341,150,31,
85,29,363,185,124,131,85,35,27,63,92,147,217,117,
87,119,81,161,178,53,45,38,50,581,661,254,87,281,
110,76,100,401,220,507,94,123,36,47,154,99,184,146,
232,26,77,193,53,264,94,110,128,87,231,110,195,156,
95,51,50,75,93,134,519,139,435,96,37,21,293,169,
70,80,104,64,210,70,48,88,67,140,26,52,45,90,
106,63,219,62,91,56,113,187,18,14,95,86,284,39,
132,31,22,69,181,167,150,117,42,14,11,73,303,109,
129,106,227,249,111,409,71,88,256,120,200,60,159,27,
63,268,389,150,311,175,136,171,116,220,30,145,95,148,
102,70,251,88,83,199,94,245,305,9,129)

************************************************************************************

plot(A,B)
abline(0,1)

At a glance, the data look very similar. Data A and B are two
measurements of the same variable but using different devices (on a
same set of subjects). Thus, I thought that a paired t-test could be
appropriate to check if the diff between measurement devices = 0.

t.test(A-B)

************************************************************************************

One Sample t-test

data:  A - B
t = 7.6276, df = 178, p-value = 1.387e-12
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
 0.002451622 0.004162903
sample estimates:
  mean of x
0.003307263

************************************************************************************
The mean diff is 0.0033 but the p-value indicates a strong evidence to
reject H0.

I was expecting to find no differences so I'm wondering whether the
t-test is the appropriate test to use. I'll appreciate any comments or
suggestions.

BR,
PM

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.