On 08/07/2010 03:08 PM, josef.kar...@phila.gov wrote:
I have read the R manual and help archives, sorry but I'm still stuck.
How would I do a t-test with an adjusted p-value?
Please be more specific about what you mean by 'adjusted p-value'. See below...
Suppose that I use t.test ( ) , with the function argument alternative =
"two.sided", and data such that degrees of freedom = 20. The function
calculates a t-statistic of 2.086, and p-value =0.05
How do I then adjust the p-value? My thought is to do
p.adjust (pt(2.086, df=20),"BH")
but that doesn't change anything (returns 0.975)
A couple things here.
1) You can get the p-value returned from t.test by inspecting the object with
?str, and noting that it's stored in an element called p-value.
So,
p.val <- t.test(extra ~ group, data = sleep)$p.value
assigns the p-value to an object called p.val.
2) You're calling p.adjust with a single p-value, so what kind of adjustment did
you have in mind? You would normally be adjusting p-values because of a multiple
comparison issue (i.e., multiple tests performed). You'd pass p.adjust the
*vector* of p-values, and a method to adjust them by. Your vector is of length
1, so in p.adjust's opinion, there is nothing to adjust for.
So, what do *you* mean by 'adjusted p-value'? `Why are you looking to adjust?`
is another way of stating that.
______________________________________________
R-help@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.
