[R] Bug in t.test?

[Johannes W. Dietrich]

Hello all,

due to unexplained differences between statistical results from 
collaborators and our lab that arose in the same large proteomics 
dataset we reevaluated the t.test() function. Here, we found a weird 
behaviour that is also reproducible in the following small test 
dataset:

Suppose, we have two vectors with numbers and some missing values 
that refer to the same individuals and that should therefore be 
evaluated with a paired t-test:

>  testdata.A <- c(1.15, -0.2, NA, 1, -2, -0.5, 0.1, 1.2, -1.4, 0.01);
>  testdata.B <- c(1.2, 1.1, 3, -0.1, 3, 1.1, 0, 1.3, 4, NA);

Then

>  print(t.test(testdata.A, testdata.B, paired=TRUE, 
>alternative="two.sided", na.action="na.pass"))

and

>  print(t.test(testdata.A, testdata.B, paired=TRUE, 
>alternative="two.sided", na.action="na.exclude"))

deliver the same p value (0.1162, identical to Excel's result).

However, after combining the two vectors with

>  testdata <- c(testdata.A, testdata.B);

and defining a criterion vector with

>  criterion <- c(0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1);

(that is the type of data layout we have in our proteomics project) 
we get a different p-value (0.01453) with

>  print(t.test(testdata ~ criterion, paired=TRUE, 
>alternative="two.sided", na.action="na.exclude")) .

The statement

>  print(t.test(testdata ~ criterion, paired=TRUE, 
>alternative="two.sided", na.action="na.pass"))

however, delivers a p-value of 0.1162 again.

With

>  print(t.test(testdata[criterion==0], testdata[criterion==1], 
>paired=TRUE, alternative="two.sided", na.action="na.exclude"))

that imitates the first form, we get again a p value of 0.1162.

What is the reason for the different p values? Should not all calls 
to t.test that exlude missing values be equivalent and therefore 
deliver the same results?

Excel, StatView and KaleidaGraph all display a p-value of 0.1162.

J. W. D.
-- 
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
-- Dr. Johannes W. Dietrich, M.D.
-- Laboratory XU44, Endocrine Research
-- Medical Hospital I, Bergmannsheil University Hospitals
-- Ruhr University of Bochum
-- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, Germany
-- Phone: +49:234:302-6400, Fax: +49:234:302-6403
-- eMail: "j.w.dietrich at medical-cybernetics.de"
-- WWW: http://medical-cybernetics.de
-- WWW: http://www.bergmannsheil.de
-- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --