[Bioc-devel] edgeR and limma Default Offsets

Ryan Thompson rct at thompsonclan.org
Thu Feb 16 08:54:22 CET 2017

They wouldn't be exactly consistent even if they used the same prior count,
since the calculations are not identical. edgeR normalizes the prior count
by each library's normalization factor so that log fold changes are always
squeezed toward zero, while voom, if I understand correctly, does not
normalize the prior count so that all log counts will be on the same scale,
at the cost of accepting some small bias in the squeezing.

On Wed, Feb 15, 2017 at 11:01 PM Dario Strbenac <dstr7320 at uni.sydney.edu.au>

> Good day,
> The cpm function in edgeR uses a default offset of 0.25 and voom in limma
> uses 0.5 (and provides no user modification) to calculate the base 2
> logarithm of the counts per million. Might these be made consistent?
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
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> Bioc-devel at r-project.org mailing list
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