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Old 03-18-2012, 11:05 AM   #1
Location: Texas

Join Date: May 2009
Posts: 32
Default edgeR Normalization question

The edgeR manual gives us three examples for DE analysis with each example normalizing the data in different manner.

In the case study 1, the Normalization was done by calcNormFactors. In the case study 2 however, only counts per million or cpm was calculated and no calcNormFactors was used. In the case study 3, both cpm and calcNormFactors was used. In this 3rd example, we are essentially modifying the data two times before performing DE analysis which is strange to me.

I basically want to perform miRNA DE analysis between two samples (each with 3 replicates). Which of the above methods is applicable for me?

Can any one please educate me? thanks in advance.
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