Dear Julie,

I am not a limma developer but it seems to me that romer() implements array
weights but not gene weights. Because the analysis of RNA-seq data requires
also gene weights, then romer() would need to be modified to accept gene
weights as well. Then voom() could be used directly. In camara()/roast()
voom based analysis gene weights are used in order to estimate the
mean-variance relationship from the data and array-weights are used to
normalize between library sizes - this generates a weights matrix that is
used in the analysis by limma functions including camera and roast.  Btw.
voom(), camera() and roast() are still part of limma but just referred to
in the edgeR manual (they can be used also with other packages).

Best Regards, Pekka


2013/6/24 <julie.leonard@syngenta.com>

> I see that the new version of edgeR has roast and camera implemented.  Is
> there a plan to implement romer in edgeR as well?
>
> Thanks!
> Julie
>
> Julie Leonard
> Computational Biologist
> Global Bioinformatics
>
> Syngenta Biotechnology, Inc.
>
> julie.leonard@syngenta.com<mailto:julie.leonard@syngenta.com>
> www.syngenta.com<http://www.syngenta.com/>
>
>
>
>
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