On Thu, Aug 18, 2011 at 1:12 PM, Ying Chen <ying.chen at="" imclone.com=""> wrote: > Hi Sean, thanks a lot for the suggestion. > > I went to your afternoon talk at the BioC2011 and I learned a lot. Great to hear! > Anyway I figured out how to install it using the source file I downloaded from Jeffry Leek's website. My computer runs windows 7 so I already have ActiveTCL installed. Thanks, Ying, for the detailed notes. Others will definitely benefit from them. >> install.packages("corpcor") >> install.packages("qvalue") >> install.packages("D:/my_sva_source_file_fold/sva_src.tar.gz",repos= NULL, type="source") > * installing *source* package 'sva' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > This is mgcv 1.7-6. For overview type 'help("mgcv-package")'. > Loading Tcl/Tk interface ... done > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > > * DONE (sva) >> library(sva) > Loading required package: corpcor > Loading required package: mgcv > This is mgcv 1.7-6. For overview type 'help("mgcv-package")'. > Loading required package: qvalue > Loading Tcl/Tk interface ... done >> > > I am a biologist and new to R and Bioconductor. I googled this forum and find a few other threads asking for help to install sva. So I hope this will help some other people new to the field. > > Ying > > > -----Original Message----- > From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis > Sent: Wednesday, August 17, 2011 4:57 PM > To: Ying Chen > Cc: bioconductor at r-project.org > Subject: Re: [BioC] sva package for R 2.13.1? > > Hi, Ying. ?SVA is not a bioconductor package, so you will probably > need to contact the author for a solution. > > Sean > > On Wed, Aug 17, 2011 at 4:49 PM, Ying Chen <ying.chen at="" imclone.com=""> wrote: >> Hi guys, >> >> Is there anyone know where I can get the correct sva package for R2.13.1? I downloaded and installed the zipped sva package from author's website, but got error message when I tried to launch it. >> >>> utils:::menuInstallLocal() >> package 'sva' successfully unpacked and MD5 sums checked >>> library(sva) >> Error: package 'sva' was built before R 2.10.0: please re-install it >>> >> >> Thanks, >> >> Ying >> Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:14}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > Confidentiality Note: > This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. > > Thank you. > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

n.b. you might also look at the 'snm' package. it has a nice vignette and does many, although not all, of the same things. likewise for Teschendorff's iSVA package on CRAN. if you try out the latter, do let folks know how it goes :-) On Wed, Aug 17, 2011 at 2:18 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > > http://leekgroup.tumblr.com/post/8223377345/at-bioc-2011-awesome- lineup-of-talks-sva-in-bioc > > Odd. > Seems there are two schools of thought on the matter (not unprecedented) > > Regardless, until the package *IS* in BioC, it's up to Jeff Leek to support > it. He seemed nice enough, why not ask him directly? > > > On Wed, Aug 17, 2011 at 2:02 PM, James W. MacDonald <jmacdon@med.umich.edu> > wrote: > >> Why don't you ask the person who wrote the package? IIRC, this isn't, nor >> has ever been a BioC package, so why ask here? >> >> Best, >> >> Jim >> >> >> On 8/17/2011 4:49 PM, Ying Chen wrote: >> >>> Hi guys, >>> >>> Is there anyone know where I can get the correct sva package for R2.13.1? >>> I downloaded and installed the zipped sva package from author's website, but >>> got error message when I tried to launch it. >>> >>> utils:::menuInstallLocal() >>>> >>> package 'sva' successfully unpacked and MD5 sums checked >>> >>>> library(sva) >>>> >>> Error: package 'sva' was built before R 2.10.0: please re-install it >>> >>>> >>>> >>> Thanks, >>> >>> Ying >>> Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:14}} >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ************************************************************ >> Electronic Mail is not secure, may not be read every day, and should not >> be used for urgent or sensitive issues >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > > > -- > If people do not believe that mathematics is simple, it is only because > they do not realize how complicated life is. > John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> > > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

I encourage people to "strongly suggest" to Jeff that he puts the package on either bioc or cran (as he should have done a while ago). AFAIK he is working on it, but any additional pressure might help :) Kasper On Wed, Aug 17, 2011 at 5:18 PM, Tim Triche, Jr. <tim.triche at="" gmail.com=""> wrote: > http://leekgroup.tumblr.com/post/8223377345/at-bioc-2011-awesome- lineup-of-talks-sva-in-bioc > > Odd. > Seems there are two schools of thought on the matter (not unprecedented) > > Regardless, until the package *IS* in BioC, it's up to Jeff Leek to support > it. ?He seemed nice enough, why not ask him directly? > > > On Wed, Aug 17, 2011 at 2:02 PM, James W. MacDonald > <jmacdon at="" med.umich.edu="">wrote: > >> Why don't you ask the person who wrote the package? IIRC, this isn't, nor >> has ever been a BioC package, so why ask here? >> >> Best, >> >> Jim >> >> >> On 8/17/2011 4:49 PM, Ying Chen wrote: >> >>> Hi guys, >>> >>> Is there anyone know where I can get the correct sva package for R2.13.1? >>> I downloaded and installed the zipped sva package from author's website, but >>> got error message when I tried to launch it. >>> >>> ?utils:::menuInstallLocal() >>>> >>> package 'sva' successfully unpacked and MD5 sums checked >>> >>>> library(sva) >>>> >>> Error: package 'sva' was built before R 2.10.0: please re-install it >>> >>>> >>>> >>> Thanks, >>> >>> Ying >>> Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:14}} >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ************************************************************ >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > > > -- > If people do not believe that mathematics is simple, it is only because they > do not realize how complicated life is. > John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >