Hi all,

I am currently using edgeR within a dog melanoma French project in order to find differentially expressed genes.

One of the first steps of edgeR is to normalize the feature count according to the library size of each sample.
I am able to find the normalized counts when I use the ‘usual’ approach in the object ‘y$pseudo.counts’ after the dispersion estimation command.
But when I use the GLM approach, I can’t find them (neither the information in the documentation nor the counts in any object produced). Where are they stored ?

For information, here is the sessionInfo() and maintainers:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US       
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US   
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.2.4  limma_3.16.8
> packageDescription('edgeR')$Maintainer
[1] "Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy\n<dmccarthy@wehi.edu.au>, Yunshun Chen <yuchen@wehi.edu.au>,\nGordon Smyth <smyth@wehi.edu.au>"

I can’t really choose the software/package versions I am using because I work on a cluster.

Cheers,
Mathieu Bahin
IGDR - Rennes (France)
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