
Sorry, found the normalized count of each gene should be calculated with the formula:

norm_counts.table <- t(t(d$pseudo.alt)*(d$samples$norm.factors))

instead of: 

(d$pseudo.alt)*(d$samples$norm.factors). 

The formula colSums(d$pseudo.alt)*d$samples$norm.factors is used to compare the total counts of each library only, not the individual genes.

Yifang
 

Yifang Tan
 		 	   		  
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