[BioC] edgeR question

Naomi Altman naomi at stat.psu.edu
Fri Jun 25 22:43:51 CEST 2010

Hi Zhe,
1. First normalize and then do the DE 
analysis.  (I found this confusing in the vignette, too.)

2. I do not suggest using FDR at this time.  The 
standard FDR computations need to be adjusted for 
count data.  I do not think this has been worked out yet.


At 12:21 PM 6/25/2010, 王孆 wrote:

>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 (>Â 
>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,
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>Bioconductor at stat.math.ethz.ch
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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