[BioC] P values on Log or Non-Log Values

[Park, Richard]

Hi Everyone, 
I am currently using the mt.teststat to calculate p-values between various samples. I was wondering if anyone knew if it was ok to run p-values on logged or non-logged values? In the past using MAS processing, I always calculated pvalues on the raw values, however I have recently switched to processing cel files through rma and the raw data produced from this processing is log base 2. 
 
My lab has noticed that log transformation Is not very visible with high p.values (above 0.1), but spreads them all over the place in the low (significant !) range. By running a t.test on loged values, it greatly enhances the significance (up to 100-fold, compared to running on straight values) when significance derives from tight distributions, but has very little or no effect when significance derives from more distant means
 
Anyone have any ideas on which method is correct? 
 
thanks, 
Richard Park 
Computational Data Analyzer
Joslin Diabetes Center