

Hello,
 
I am learning edgeR and would like to use it dealing with my Tag-seq and RNA-seq data. I have several questions:
 
1. Does the DE analysis using common dispersion or moderated tagwise dispersions use the TMM method for normalization?  I am not sure the relationship between Setion 6 (Normalization) and the following sections in the user manual. I suppose I should normalize the data first, and then perform DE analysis.
 
2. Do you suggest to use P-value < 0.01? What about FDR < 0.05? After saving de.tagwise (> write.table(de.com[[1]], file = "/Users/Zhe/edgeR/page7", sep = "\t")), I found there is not a column of the FDR. How to calculate the FDR for each gene and save it in the output file.
 
Thanks a lot.
Best wishes,
 
Zhe
 


      
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