 
 
Hello,
 
 
I have fit a group means parameterization to my three samples: A, B, C (fit1).  I used contrasts.fit to fit my contrasts of interest: B-A, and C-A (fit2).  My question: does fit2$F.p.value apply to the differences between the three samples A, B, and C (similar to a one-way ANOVA) or does it apply to
the differences between the two contrasts B-A and C-A?  I really need someone to clarify this point for me before I go on and select differentially expressed genes.  In my case treatments B and C are very similar so this point is almost mute.  However, I will be analyzing data sets in the future
where treatments B and C are very different making my question very important.     
 
Scott Ochsner
Baylor College of Medicine
One Baylor Plaza
Houston, TX. 77030
 
 
thanks,
 
S 
 
 
Sent for S. Ochsner by TAM 

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