[BioC] negative values in raw data

[Guillaume Deplaine]

Hi,

    I downloaded data on the GEO web site and now, I try to analyze them 
with R 2.0.1 for windows XP but in this dataset, there is a lot of negative 
values. So when I normalyze with log2 transformation, R produced NaNs. I 
understand why but after, when I want to calculate p-value with the 
parametric t test, R can't. I tried to write 0 where there is a negative 
value :  R calculate p-value and q-value but all of q-value are at 1.

    Is there someone to help me.
Thanks a lot