romer implementation in edgeR
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Pekka Kohonen ▴ 190
@pekka-kohonen-5862
Last seen 4.6 years ago
Sweden
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=""/> > > > > > This message may contain confidential information. If ...{{dropped:13}}
limma edgeR CAMERA limma edgeR CAMERA • 1.4k views
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@gordon-smyth
Last seen 8 hours ago
WEHI, Melbourne, Australia

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

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Thank you. I have had good success getting roast to work in edgeR. Julie Leonard Computational Biologist Global Bioinformatics Syngenta Biotechnology, Inc. 3054 E. Cornwallis Rd. Research Triangle Park, NC 27709 USA phone 1-919-281-7449 julie.leonard at syngenta.com www.syngenta.com -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Thursday, July 04, 2013 7:38 PM To: Pekka Kohonen Cc: Yunshun Chen; Bioconductor mailing list; Leonard Julie USRE Subject: romer implementation in edgeR 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:14}}
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