[R] help in interpreting paired t-test

[(Ted Harding)]

As can be seen by plotting as follows:

  plot(A,B,pch="+",col="blue")   ## The raw data

  plot(A,B-A,pch="+",col="blue") ## The differences versus A
  lines(c(0,0.7),c(0,0))

Ted.

On 20-Sep-11 17:54:15, Timothy Bates wrote:
> Yes, in over 3/4s of the data points A is > B
 which suggests the A
> measure is reading higher than the B measuring system.
> 
> length(A[A>B])/length(A)
> 
> 
> On 20 Sep 2011, at 6:46 PM, Pedro Mardones wrote:
> 
>> 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.

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Date: 20-Sep-11                                       Time: 19:15:47
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