Question

Install devel version of edgeR

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Gordon Smyth 51k

@gordon-smyth

Last seen 53 minutes ago

WEHI, Melbourne, Australia

Dear Javier, This is a question for the Bioc managers, but the following page might answer your question: http://www.bioconductor.org/developers/useDevel/ Best wishes Gordon On Thu, 13 Sep 2012, Javier Sim?n-S?nchez wrote: > Hello Gordon, > > Thanks a lot for your reply. > > How can I upgrade to the latest version of edge R? I have checked on the > list and it looks like i need version 2.99.3. However, the one you provide > at http://www.bioconductor.org/packages/2.10/bioc/html/edgeR.html is > edgeR_2.6.12. How can I get the needed version? > > Thanks a lot for your help. > > On Thu, Sep 13, 2012 at 2:43 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> Dear Javier, >> >> This error has been discused a number of times on this list. The solution >> is to upgrade edgeR to the current devel version. >> >> Also please see the Bioconductor posting guide: >> >> http://www.bioconductor.org/**help/mailing- list/posting-**guide/<http: www.bioconductor.org="" help="" mailing-list="" posting-guide=""/> >> >> Best wishes >> Gordon >> >> Date: Tue, 11 Sep 2012 13:04:55 +0200 >>> From: Javier Sim?n-S?nchez <simonsanchezj at="" gmail.com=""> >>> To: bioconductor at r-project.org >>> Subject: [BioC] edgeR GLM error >>> >>> Hello, >>> My name is Javier Sim?n Seanchez and I'm a post-doc at the VUmc in >>> Amsterdam. >>> >>> The reason of this e-mail is that im running edgeR in an expression >>> dataset >>> and getting the following error when calculating the GLM common >>> dispersion: >>> >>> *Error in beta[k, ] <- betaj[decr, ] : >>> NAs are not allowed in subscripted assignments >>> * >>> >>> Im running cases versus controls and I want to modulate for different >>> tissues. How can I overcome this error? >>> >>> Thanks a lot in advance >>> >>> -- >>> Javier Simon-Sanchez >>> >>> >> ______________________________**______________________________**___ _______ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________**______________________________**___ _______ > > > > > -- > Javier Simon-Sanchez > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}

edgeR edgeR • 1.1k views

ADD COMMENT • link 12.2 years ago Gordon Smyth 51k

score 0 · Answer 1 · 2012-09-14

Alternatively you can download from: http://bioconductor.org/packages/2.11/bioc/html/edgeR.html Gordon On Fri, 14 Sep 2012, Gordon K Smyth wrote: > Dear Javier, > > This is a question for the Bioc managers, but the following page might answer > your question: > > http://www.bioconductor.org/developers/useDevel/ > > Best wishes > Gordon > > On Thu, 13 Sep 2012, Javier Sim?n-S?nchez wrote: > >> Hello Gordon, >> >> Thanks a lot for your reply. >> >> How can I upgrade to the latest version of edge R? I have checked on the >> list and it looks like i need version 2.99.3. However, the one you provide >> at http://www.bioconductor.org/packages/2.10/bioc/html/edgeR.html is >> edgeR_2.6.12. How can I get the needed version? >> >> Thanks a lot for your help. >> >> On Thu, Sep 13, 2012 at 2:43 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: >> >>> Dear Javier, >>> >>> This error has been discused a number of times on this list. The solution >>> is to upgrade edgeR to the current devel version. >>> >>> Also please see the Bioconductor posting guide: >>> >>> http://www.bioconductor.org/**help/mailing- list/posting-**guide/<http: www.bioconductor.org="" help="" mailing-list="" posting-guide=""/> >>> >>> Best wishes >>> Gordon >>> >>> Date: Tue, 11 Sep 2012 13:04:55 +0200 >>>> From: Javier Sim?n-S?nchez <simonsanchezj at="" gmail.com=""> >>>> To: bioconductor at r-project.org >>>> Subject: [BioC] edgeR GLM error >>>> >>>> Hello, >>>> My name is Javier Sim?n Seanchez and I'm a post-doc at the VUmc in >>>> Amsterdam. >>>> >>>> The reason of this e-mail is that im running edgeR in an expression >>>> dataset >>>> and getting the following error when calculating the GLM common >>>> dispersion: >>>> >>>> *Error in beta[k, ] <- betaj[decr, ] : >>>> NAs are not allowed in subscripted assignments >>>> * >>>> >>>> Im running cases versus controls and I want to modulate for different >>>> tissues. How can I overcome this error? >>>> >>>> Thanks a lot in advance >>>> >>>> -- >>>> Javier Simon-Sanchez >>>> >>>> >>> ______________________________**______________________________**__ ________ >>> The information in this email is confidential and intended solely for the >>> addressee. >>> You must not disclose, forward, print or use it without the permission of >>> the sender. >>> ______________________________**______________________________**__ ________ >> >> >> >> >> -- >> Javier Simon-Sanchez > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}