[Bioc-devel] edgeR and limma Default Offsets

[Steve Lianoglou]

Hi all,

For a bit more background (and for the sake of posterity), Gordon has
previously discussed the rationale of tunable (or not) prior.counts in
edgeR::cpm and voom in this support forum thread:

https://support.bioconductor.org/p/59846/#59917

-steve

On Thu, Feb 16, 2017 at 8:00 PM, Dario Strbenac
<dstr7320 at uni.sydney.edu.au> wrote:
> Good day,
>
> Now I notice the differences in how the prior counts are applied. In edgeR's cpm:
>
> prior.count.scaled <- lib.size/mean(lib.size) * prior.count
> lib.size <- lib.size + 2 * prior.count.scaled
>     ...                        ...
> t(x) + prior.count.scaled
>
> but in limma's voom:
>
> t(counts + 0.5)/(lib.size + 1)
>
> Basically, the values added to the counts and the library size ignore the library size of each sample in the voom function.
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
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-- 
Steve Lianoglou
Bioinformatics Scientist
Cancer Immunology
Genentech