[BioC] romer implementation in edgeR

[Gordon K Smyth]

Dear Julie and Pekka,

Pekka is right that the camera, roast and romer functions are part of 
limma, and that romer() doesn't allow gene weights and so doesn't work 
with the voom() pipeline, at least not yet.  We have been recommending 
voom() as the means to access gene set and expression signature testing 
for RNA-seq data, so the lack of romer functionality does represent a 
limitation.

However we quietly made a new development in the latest versions of limma 
and edgeR, so that the roast() and camera() functions are now generic 
functions defined in limma, and so that edgeR defines DGEList methods for 
both roast and camera.  This means that edgeR can now do gene set testing 
directly without going through voom.  The DGEList methods do not require 
weights to be defined.  This is I think what Julie is asking about.

To Julie: we ourselves use camera() and roast() much more in our own work 
than we do romer() but, if you have a need for romer(), we can easily 
implement a romer method in edgeR also.

Best wishes
Gordon

> Date: Wed, 3 Jul 2013 16:05:14 +0200
> From: Pekka Kohonen <pkpekka at gmail.com>
> To: julie.leonard at syngenta.com
> Cc: Bioconductor <bioconductor at r-project.org>
> Subject: Re: [BioC] romer implementation in edgeR
>
> 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 at 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 at syngenta.com
>> www.syngenta.com

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