[BioC] Getting edgeR normalized counts within the GLM approach

Ryan rct at thompsonclan.org
Tue Apr 8 18:23:13 CEST 2014


I believe the pseudo counts are used internally for some of the 
dispersion estimation methods, but are not indented for other uses. The 
standard way to get normalized feature abundances from a DGEList is to 
use the cpm function.


On Tue Apr  8 08:03:06 2014, Mathieu Bahin wrote:
> 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$pseudo.counts’ after the dispersion estimation command.
> But when I use the GLM approach, I can’t find them (neither the information in the documentation nor the counts in any object produced). Where are they stored ?
> For information, here is the sessionInfo() and maintainers:
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
>   [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
>   [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] edgeR_3.2.4  limma_3.16.8
>> packageDescription('edgeR')$Maintainer
> [1] "Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy\n<dmccarthy at wehi.edu.au>, Yunshun Chen <yuchen at wehi.edu.au>,\nGordon Smyth <smyth at 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)
> 	[[alternative HTML version deleted]]
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