Dear all, this might be a really, really stupid question, but I can't figure it out. I have created an annotation.db for an agilent one color 4x44K zebrafish array, but I can't figure out how to load it into R afterwards. Can anyone help ? kind regards, Mayra -- Mayra Eduardoff Institute of Molecular Biology University of Innsbruck Viktor-Franz Hess Haus Technikerstrasse 25 6020 Innsbruck Tel: +43 512 507 6286 email: mayra.eduardoff@student.uibk.ac.at [[alternative HTML version deleted]]

On Tue, Aug 4, 2009 at 12:11 PM, Mayra Eduardoff <mayra.eduardoff@gmail.com>wrote: > Dear all, > this might be a really, really stupid question, but I can't figure it out. > I have created an annotation.db for an agilent one color 4x44K zebrafish > array, but I can't figure out how to load it into R afterwards. Can anyone > help ? > You need to "install" it, first. Then, you can load it. Sean [[alternative HTML version deleted]]

On Tue, Aug 4, 2009 at 12:34 PM, Mayra Eduardoff <mayra.eduardoff@gmail.com>wrote: > thanks for the quick answer, yes, but how do I install it ? > install.package ? but what is my repos ? I don t have a binary file or do I > ? I just don t get it .... > doing ?install.packages will get you help for install.packages(). However, install.packages() with repos=NULL and the file path of the package should do it. It is probably not a binary package. Sean > > > > On Tue, Aug 4, 2009 at 6:17 PM, Sean Davis <seandavi@gmail.com> wrote: > >> >> >> On Tue, Aug 4, 2009 at 12:11 PM, Mayra Eduardoff < >> mayra.eduardoff@gmail.com> wrote: >> >>> Dear all, >>> this might be a really, really stupid question, but I can't figure it >>> out. >>> I have created an annotation.db for an agilent one color 4x44K zebrafish >>> array, but I can't figure out how to load it into R afterwards. Can >>> anyone >>> help ? >>> >> >> You need to "install" it, first. Then, you can load it. >> >> Sean >> >> >> > > > -- > Mayra Eduardoff > Institute of Molecular Biology > University of Innsbruck > Viktor-Franz Hess Haus > Technikerstrasse 25 > 6020 Innsbruck > Tel: +43 512 507 6286 > email: mayra.eduardoff@student.uibk.ac.at > > [[alternative HTML version deleted]]

On Tue, Aug 4, 2009 at 12:55 PM, Mayra Eduardoff <mayra.eduardoff@gmail.com>wrote: > I ve read the help and tried before and it is not working... > > the db is in my working directoy > > install.packages("zfv2.db", pkgs="zfv2.db",repos=NULL) > install.packages(pkgs="zfv2.db.tar.gz",repos=NULL) You will need to tar and compress the package directory, I think. Sean > > get a german error message, so I guess that won't help > > Fehler in if (ok) { : Fehlender Wert, wo TRUE/FALSE nötig ist > > > > > On Tue, Aug 4, 2009 at 6:44 PM, Sean Davis <seandavi@gmail.com> wrote: > >> >> >> On Tue, Aug 4, 2009 at 12:34 PM, Mayra Eduardoff < >> mayra.eduardoff@gmail.com> wrote: >> >>> thanks for the quick answer, yes, but how do I install it ? >>> install.package ? but what is my repos ? I don t have a binary file or do >>> I ? I just don t get it .... >>> >> >> doing ?install.packages will get you help for install.packages(). >> >> However, install.packages() with repos=NULL and the file path of the >> package should do it. It is probably not a binary package. >> >> Sean >> >> >> >>> >>> >>> >>> On Tue, Aug 4, 2009 at 6:17 PM, Sean Davis <seandavi@gmail.com> wrote: >>> >>>> >>>> >>>> On Tue, Aug 4, 2009 at 12:11 PM, Mayra Eduardoff < >>>> mayra.eduardoff@gmail.com> wrote: >>>> >>>>> Dear all, >>>>> this might be a really, really stupid question, but I can't figure it >>>>> out. >>>>> I have created an annotation.db for an agilent one color 4x44K >>>>> zebrafish >>>>> array, but I can't figure out how to load it into R afterwards. Can >>>>> anyone >>>>> help ? >>>>> >>>> >>>> You need to "install" it, first. Then, you can load it. >>>> >>>> Sean >>>> >>>> >>>> >>> >>> >>> -- >>> Mayra Eduardoff >>> Institute of Molecular Biology >>> University of Innsbruck >>> Viktor-Franz Hess Haus >>> Technikerstrasse 25 >>> 6020 Innsbruck >>> Tel: +43 512 507 6286 >>> email: mayra.eduardoff@student.uibk.ac.at >>> >>> >> > > > -- > Mayra Eduardoff > Institute of Molecular Biology > University of Innsbruck > Viktor-Franz Hess Haus > Technikerstrasse 25 > 6020 Innsbruck > Tel: +43 512 507 6286 > email: mayra.eduardoff@student.uibk.ac.at > > [[alternative HTML version deleted]]

To build binaries you use R CMD INSTALL --build which will result in a binary package in your R_HOME/bin directory, as well as the package being installed. Best, Jim James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 >>> Mayra Eduardoff <mayra.eduardoff at="" gmail.com=""> 08/05/09 4:19 AM >>> Ok, this might be really obvious, but I finally managed. I am using R on Windows at the moment, so I had to download the Rtools from http://www.murdoch-sutherland.com/Rtools/Rtools.txt so that i can compile and install tar.gz packages. then I compiled the .db and installed it using R CMD INSTALL. I still don t know how to compile windows binaries... but well it works this way. thanks again for your help ! kind regards mayra On Tue, Aug 4, 2009 at 6:59 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > > > On Tue, Aug 4, 2009 at 12:55 PM, Mayra Eduardoff < > mayra.eduardoff at gmail.com> wrote: > >> I ve read the help and tried before and it is not working... >> >> the db is in my working directoy >> >> install.packages("zfv2.db", pkgs="zfv2.db",repos=NULL) >> > > install.packages(pkgs="zfv2.db.tar.gz",repos=NULL) > > You will need to tar and compress the package directory, I think. > > Sean > > > >> >> get a german error message, so I guess that won't help >> >> Fehler in if (ok) { : Fehlender Wert, wo TRUE/FALSE n?tig ist >> >> >> >> >> On Tue, Aug 4, 2009 at 6:44 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >>> >>> >>> On Tue, Aug 4, 2009 at 12:34 PM, Mayra Eduardoff < >>> mayra.eduardoff at gmail.com> wrote: >>> >>>> thanks for the quick answer, yes, but how do I install it ? >>>> install.package ? but what is my repos ? I don t have a binary file or >>>> do I ? I just don t get it .... >>>> >>> >>> doing ?install.packages will get you help for install.packages(). >>> >>> However, install.packages() with repos=NULL and the file path of the >>> package should do it. It is probably not a binary package. >>> >>> Sean >>> >>> >>> >>>> >>>> >>>> >>>> On Tue, Aug 4, 2009 at 6:17 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >>>> >>>>> >>>>> >>>>> On Tue, Aug 4, 2009 at 12:11 PM, Mayra Eduardoff < >>>>> mayra.eduardoff at gmail.com> wrote: >>>>> >>>>>> Dear all, >>>>>> this might be a really, really stupid question, but I can't figure it >>>>>> out. >>>>>> I have created an annotation.db for an agilent one color 4x44K >>>>>> zebrafish >>>>>> array, but I can't figure out how to load it into R afterwards. Can >>>>>> anyone >>>>>> help ? >>>>>> >>>>> >>>>> You need to "install" it, first. Then, you can load it. >>>>> >>>>> Sean >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Mayra Eduardoff >>>> Institute of Molecular Biology >>>> University of Innsbruck >>>> Viktor-Franz Hess Haus >>>> Technikerstrasse 25 >>>> 6020 Innsbruck >>>> Tel: +43 512 507 6286 >>>> email: mayra.eduardoff at student.uibk.ac.at >>>> >>>> >>> >> >> >> -- >> Mayra Eduardoff >> Institute of Molecular Biology >> University of Innsbruck >> Viktor-Franz Hess Haus >> Technikerstrasse 25 >> 6020 Innsbruck >> Tel: +43 512 507 6286 >> email: mayra.eduardoff at student.uibk.ac.at >> >> > -- Mayra Eduardoff Institute of Molecular Biology University of Innsbruck Viktor-Franz Hess Haus Technikerstrasse 25 6020 Innsbruck Tel: +43 512 507 6286 email: mayra.eduardoff at student.uibk.ac.at [[alternative HTML version deleted]] ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues