Hello forum,
I was reading some of the theory behind cuffdiff and how it calculates
for DE genes.

My question:

if I do not have replicates, how does cuffdiff do the test statistic
which is dependent on the variance?
The manual says "Note that in order to calculate the test statistic T,
we need to know the variance of the expression level in each
Doesn't this mean that I am supposed to have replicates?Otherwise how
can we have variance if we only have ONE SAMPLE?

I would appreciate if anyone could explainthis to me. Ciffdiff
caclulates DE even when I give him one sample agaist another one...how
reliable is the reult?


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