[R] changing the default repositories
Hello, Is it possible to change the default repositories? I've already changed the list in the repositories file under etc/ this is how my repositories file under R/etc looks like: row namemenu_nameURLdefaultsourcewin.binary mac.binary CRANCRAN@CRAN@TRUETRUETRUETRUE BioCBioconductorhttp://www.bioconductor.orgTRUETRUE TRUEFALSE CRANextraCRAN (extras)http://www.stats.ox.ac.uk/pub/RWinTRUE FALSETRUEFALSE OmegahatOmegahathttp://www.omegahat.org/RTRUETRUETRUE FALSE BioCcdfBIOCcdf http://www.bioconductor.org/packages/data/annotation/1.7TRUETRUE TRUEFALSE BioCCoursesBioCcourseshttp://www.bioconductor.org/repository/Courses TRUETRUETRUEFALSE every time i start R it shows me only the first two lines as default instead of all of them. Is there a possibility to change it in the Rprofile.site or in the repositories files, so R will always use the complete list as a default? Thx for any help. Assa -- Assa Yeroslaviz Loetzener Str. 15 51373 Leverkusen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] design matrix and coefficients
Hey, As a beginner to the limma package I tried to understand how to define a design matrix. I did both experiment examples in the Limma user's Guide manual. Afterwards I wanted to do it with my own data. Here I encounter a few problems. As an example I used four Control samples and 4 treated samples. 1. This is how my target files looks like: filenametreated time.h conc. ctrl_1.cel no240 ctrl_2.cel no240 ctrl_3.cel no240 ctrl_4.cel no240 treat_100_1.cel yes24100 treat_100_2.cel yes24100 treat_1000_3.celyes241000 treat_1000_4.celyes241000 2. I would like to create a design matrix to compare all 4 wt files with all 4 ctrl files. But I also want to see the differences between the two concentrations (100, 1000). I have a problem creating the different coefficients. How do I choose which coefficient to build? I would be happy for any help. I didn't find much information about the limma package and the affymetrix (single-channel) chips. If you can help me looking for general information I'll be also grateful. THX, Assa -- Assa Yeroslaviz Loetzener Str. 15 51373 Leverkusen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Unix proxy and firewall problems
I was trying to install R on a unix server. Because of a firewall i can't install biocLite for working with Bioconductor. With windows it wasn't a problem. I used the option '--internet2' to bypass the firewall. I don't have any idea, how to do it with unix. I tried to set my proxy Sys.putenv(http_proxy=http...:8080) Sys.getenv(http_proxy) http_proxy http://...:8080; http://by-cache.bayer-ag.com:8080/ but than by try to use the source command to download the bioC.R script I'm getting the message: source(http:/bioconductor.org/getBioC.R) Error in file(file, r, encoding = encoding) : unable to open connection In addition: Warning message: cannot open file 'http:/bioconductor.org/getBioC.R' Is there a possibility to change the proxy setting after the programm is already running or do i need to do it before? THX Assa -- Assa Yeroslaviz Loetzenerstr. 15 51373 Leverkusen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
