[BioC] edgeR question

Gordon K Smyth smyth at wehi.EDU.AU
Sat Jun 26 11:01:01 CEST 2010

Dear Zhe,

To get FDR, you must use the topTags() function.  Is your de.com object a 
deDGEList object?  If it is, then

   top <- topTags(de.com, n=Inf)
   write.table(top$table, file="yourfile.txt")

will do what you want.  (I can't tell you what level of FDR to use as your 
cutoff though, that's up to you.)

Naomi, I don't know of any problem with FDR from edgeR.  It should work 
just fine.

Best wishes

Associate Professor Gordon K Smyth,
NHMRC Senior Research Fellow,
Bioinformatics Division, 
Walter and Eliza Hall Institute of Medical Research, 
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth at wehi.edu.au

------------ original message ---------------
[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,  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 (>
>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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