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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