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Question: DEseq version and R version compatibility
0
6.4 years ago by
José Luis Lavín270 wrote:
deseq • 1.2k views
modified 6.4 years ago by Thomas Girke1.7k • written 6.4 years ago by José Luis Lavín270
Answer: DEseq version and R version compatibility
0
6.4 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:
Answer: DEseq version and R version compatibility
0
6.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
Howdy, On Thu, Oct 4, 2012 at 9:41 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, Oct 4, 2012 at 9:30 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: >> Hello Sean, >> >> The main problem with updating the R version of the servers is that I'm not >> the SysAdmin, and he told me that they couldn't update it at the moment >> because they have some processes and pipelines that need the old R version >> (2.13), so he can't update it (weird, isn't it?). That's why I was looking >> for such strange compatibility... >> Anyway, due to my current low level on R scripting, when I come across a >> command that isn't functional I don't really know what to do but trying to >> use another manual version hoping the code there will fix it...but I've had >> no luck with that at the moment. That's why I asked about this. >> I'll keep trying to make DEseq work, but I begin to feel stupid, reading >> everybody seems to be able to run it except myself. > > If you have a good relationship with your sysadmin, ask him/her to > help you to install R in your home directory. This is not hard to do > (hopefully, for a sysadmin) and will allow you to run a different > version of R than that already installed on the system. Really, doing > this will be much better than copying code from various versions of > packages to "just make it work". In fact, I bet you can do it w/o a sysadmin. Let's assume your username is jose (1) Log into your compute server (2) cd ~ ## you're likely already there Create directories to put the source code in as well as the compiled R (3) mkdir tmp (4) mkdir -p R/R-2.15 ## R will be installed here Let's get the source code and put it into tmp (5) cd tmp Get the code with curl or wget (whichever your system has) (6a) curl -O http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz ## or ## (6b) wget http://cran.r-project.org/src/base/R-2/R-2.15.1.tar.gz Open it up, configure, compile, install (7) tar xvfz R-2.15.1.tar.gz (8) cd R-2.15.1 ## This is where you tell it where to install the new version of R ## Since it is in your home directory, your sysadmin doesn't need to be there ## and it won't affect anybody else's stuff (9) ./configure --prefix=/home/jose/R/R-2.15 (10) make && make install ... now you wait a while until it's all done ... Start R: (11) ~/R/R-2.15/bin/R biocLite() your packages and have fun. You may want to add /home/R/R-2.15/bin to your PATH -- you can ask your sysadmin how to do that, if you like ;-) -seve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
Hi, On Thu, Oct 4, 2012 at 10:42 AM, Jos? Luis Lav?n <jluis.lavin at="" unavarra.es=""> wrote: > Thank you everybody for your advice and opinions. I just wanted to be able > to analyze my DE data and since I couldn't change R versions due to issues > beyond my grasp... > So, since I've the current R version in windows, I'll try to follow the > newest manual commands there. > ?May any of you tell me which is the last version of DEseq manual? It's always: http://bioconductor.org/packages/release/bioc/html/DESeq.html *currently* that is the same as: http://bioconductor.org/packages/2.11/bioc/html/DESeq.html Because 2.11 is the current release. The one that goes under active development which will be released with the *next* (always next) version of R/bioconductor is: http://bioconductor.org/packages/devel/bioc/html/DESeq.html HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
Answer: DEseq version and R version compatibility
0
6.4 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Answer: DEseq version and R version compatibility
0
6.4 years ago by
Spain
José Luis Lavín10 wrote: