Hi guys,
I encounter this kind question quite a few times now and never have a good answer. Say we have the expression data (microarray or RNAseq) of gene A for both tumor and normal samples. The task is to detect how many tumor samples have gene A over-expressed. I had tried to use mean+2*stdev of normal samples, Q3+3*IQR of normal samples as cutoffs. But depending on normal sample data distribution, one cut-off could be more stringent in one case, but less stringent in another case.
Your guys must have met this kind question before, what kind cutoff do you use and why? What do you do when you have very few (1,2,3,4,..) or no normal samples?
Thanks,
Ying 		 	   		  
	[[alternative HTML version deleted]]

