[R] Paired t-tests

[Marc Schwartz]

On Aug 15, 2010, at 9:05 AM, R Help wrote:

> Hello List,
> 
> I'm trying to do a paired t-test, and I'm wondering if it's consistent
> with equations.  I have a dataset that has a response and two
> treatments (here's an example):
> 
>   ID trt order          resp
> 17  1   0     1  0.0037513592
> 18  2   0     1  0.0118723051
> 19  4   0     1  0.0002610251
> 20  5   0     1 -0.0077951450
> 21  6   0     1  0.0022339952
> 22  7   0     2  0.0235195453
> 
> The subjects were randomized and assigned to receive either the
> treatment or the placebo first, then the other.  I know I'll
> eventually have to move on to a GLM or something that incorporates the
> order, but for now I wanted to start with a simple t.test.  My problem
> is that, if I get the responses into two vectors x and y (sorted by
> ID) and do a t.test, and then compare that to a formula t.test, they
> aren't the same.
> 
>> t.test(x,y,paired=TRUE)
> 
> 	Paired t-test
> 
> data:  x and y
> t = -0.3492, df = 15, p-value = 0.7318
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.010446921  0.007505966
> sample estimates:
> mean of the differences
>           -0.001470477
> 
>> t.test(resp~trt,data=dat1[[3]],paired=TRUE)
> 
> 	Paired t-test
> 
> data:  resp by trt
> t = -0.3182, df = 15, p-value = 0.7547
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> -0.007096678  0.005253173
> sample estimates:
> mean of the differences
>          -0.0009217521
> 
> What I'm assuming is that the equation isn't retaining the inherent
> order of the dataset, so the pairing isn't matching up (even though
> the dataset is ordered by ID).  Is there a way to make the t.test
> retain the correct ordering?
> 
> Thanks,
> Sam


See this thread from just 2 days ago:

  https://stat.ethz.ch/pipermail/r-help/2010-August/249068.html

perhaps focusing on Thomas' reply, which is the next post in the thread.

Bottom line, don't use the formula method for a paired t test.

HTH,

Marc Schwartz