Question: P values on Log or Non-Log Values

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Park, Richard •

**220**wrote: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

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modified 16.3 years ago
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James W. MacDonald ♦

**50k**• written 16.3 years ago by Park, Richard •**220**