[BioC] mt.teststat

[Park, Richard]

Hello Everyone, 

I was wondering if anyone could interpret the raw p-values calculated using mt.teststat() (this function is part of the multtest package). I am using the following lines:

 

## To Calculate two-sided unequal variance t test values ##

teststat <- mt.teststat(compSet, label, test="t", nonpara="n")
rawp <- 2 * (1-pnorm(abs(teststat)))

 

I am keeping track of the rawp values between all possible comparisons of samples. 

However, I have not been able to completely decipher the values that are coming out of this combination. 

 

Example:

WT = 58.286, 48.842, 51.108

KO = 7.486, 6.373, 7.899

 

The p value calculated using "test_t.test(x[k,],xr[k,],paired=F,var.equal=F)" is 0.003219981, which is the same value that is calculated using the t.test within Excel. Mt.teststat() produces a value of 0.00000000 (basically 0, I'm not sure if it is lack of precision?). Does anyone understand why the pvalue generated from mt.teststat() is so much smaller than the traditional t.test() and what this means? 

 

Thank you, 

Richard Park 

Computational Data Analyzer

Joslin Diabetes Center