
Hi, I'm currently using LIMMA to analyze two groups, wt vs treatment group. LIMMA says gene A is significantly different between the two groups, p=10E-6, but when I do a simple t-test I am unable to get such a significant p-value. 

For example my normalized values for ProbeID:A may be as followed:
wt - 4.8, 5.1, 5.7
treatment - 8.1, 9.8, 7

if I do >t.test(wt, treatment) I don't get a p-value as low as what is observed in the limma top table. Why would this happen?



Thanks for the help,


-Kripa
 		 	   		  
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