[BioC] How do I get p-values from multtest?

[michael watson (IAH-C)]

Hi

I want to calcualte p-value for my matrix of gene expression data, based
on t-tests, which are adjusted for the FDR (according to Benjamini and
Hochberg 1995).

In the multtest package we have mt.teststat(), which tells me how to
calculate the t statistic for each of the rows in my data frame, and we
have mt.rawp2adjp(), which converts raw p-values into adjusted p-values.

So there is a missing step - the first function tells me how to create
t.  I then need to access the p-values for this t statistic, and then go
on to convert them into adjusted p-values.

Now, the documentation for mt.maxT() and mt.minP() *suggests* that raw
p-values *can* be obtained from these functions.  However, when running
them and then comparing the $rawp slots to the p-values achieved by
running t.test(), I find that these rawp values *do not* correspond to
the equivalent p-values outputted by t.test.

SO, what I now plan on doing is:

1) iterating through my matrix myself, running t.test() on each row, and
storing the p-values
2) using these p-values as an input to mt.rawp2adjp() to create a list
of adjusted p-values
3) mapping these adjusted p-values back onto my original data matrix

So, I come to my questions:

1) can anyone tell me how to get raw p-values for the t-statistic using
multtest? 
2) as the documentation for mt.rawp2adjp() says "This function computes
adjusted p-values for simple multiple testing procedures from a vector
of raw (unadjusted) p-values", I presume plugging in p-value directly
from t.test() is perfectly valid?

Thanks

Mick