biobase
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tulay akal ▴ 10
@tulay-akal-4724
Last seen 9.6 years ago
Hi, i am using R for my master thesis, and i need to install the packages affy_1.6.7, biobase_1.5.12, 1.8.0, 2.0.1, 2.2.2, smida_0.1, repostools_1.5.2, lars_0.9-5 and hgu95acdf_1.10.0. im having troubles with loading package biobase. ive tried R versions 2.0.1, 2.1.0, 2.9.0 and 2.12.0. i couldnt install and load all the packages in single version, and also even when i could install biobase successfully, i couldnt find it in the packages list to load. and by this way i can not use affy. however the surprising thing is that when i do these with a computer running xp, R 2.1.0 sucessfully installs and loads all the packages. i am running 32 bit vista. is this the problem? i dont wanna change my operating system. i really appreciate your help Tulay AkalResearch Assistant Middle East Technical University, Turkey [[alternative HTML version deleted]]
Biobase affy Biobase affy • 780 views
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@steve-lianoglou-2771
Last seen 13 months ago
United States
Hi, On Mon, Jun 27, 2011 at 6:24 PM, tulay akal <tulay_210 at="" yahoo.com.tr=""> wrote: > Hi, i am using R for my master thesis, and i need to install the packages affy_1.6.7, biobase_1.5.12, 1.8.0, 2.0.1, 2.2.2, smida_0.1, repostools_1.5.2, lars_0.9-5 and hgu95acdf_1.10.0. im having troubles with loading package biobase. ive tried R versions 2.0.1, 2.1.0, 2.9.0 and 2.12.0. i couldnt install and load all the packages in single version, and also even when i could install biobase successfully, i couldnt find it in the packages list to load. and by this way i can not use affy. however the surprising thing is that when i do these with a computer running xp, R 2.1.0 sucessfully installs and loads all the packages. i am running 32 bit vista. is this the problem? i dont wanna change my operating system. i really appreciate your help This doesn't really address your question at all, but why do you think you need to get all of these dependencies "just so"? You'll probably have a lot less frustration if you just use the latest version of R with the latest release of the packages you mention .. and since it seems like you're doing your master thesis *now*, as opposed to XX years ago when those versions where the most recent, it seems the most sense to be using the latest and greatest :-) Was there some functionality in one of those older package that you feel like went missing? Maybe it'll be easier to approach your problem from this route ... Also -- for when you get your stuff up and running: I'd suggest using the glmnet package instead of lars. glmnet provides the lasso, and you'll get the "elasticnet" for free, which you might like to experiment with. Hope that helps, -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
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@martin-morgan-1513
Last seen 6 weeks ago
United States
On 06/27/2011 03:24 PM, tulay akal wrote: > Hi, i am using R for my master thesis, and i need to install the > packages affy_1.6.7, biobase_1.5.12, 1.8.0, 2.0.1, 2.2.2, smida_0.1, > repostools_1.5.2, lars_0.9-5 and hgu95acdf_1.10.0. im having troubles > with loading package biobase. ive tried R versions 2.0.1, 2.1.0, > 2.9.0 and 2.12.0. i couldnt install and load all the packages in > single version, and also even when i could install biobase > successfully, i couldnt find it in the packages list to load. and by > this way i can not use affy. however the surprising thing is that > when i do these with a computer running xp, R 2.1.0 sucessfully > installs and loads all the packages. i am running 32 bit vista. is > this the problem? i dont wanna change my operating system. i really > appreciate your help Listing multiple versions of Biobase is confusing to me. The idea is that specific package 'minor' versions of Bioconductor packages (e.g., Biobase 1.5.*) work with particular R releases. Doing a bit of detective work, I visited http://bioconductor.org/help/ and in the 'Previous Versions' box I clicked on the 1.6 (2.1) link. This shows that for R-2.1, I would expect affy 1.6.7, Biobase 1.5.12. reposTools 1.5.19; lars and smida are CRAN packages and are managed in a different way but available from CRAN's archive. Focusing on the Bioconductor packages, Downloaded the Windows binary of R-2.1.1 (or the version appropriate for your operating system; there may be significant issues with building old R versions on recent OS versions) from CRAN and then source("http://bioconductor.org/biocLite.R") biocLite(c("affy", "Biobase")) library(Biobase) What happens? If you are wanting to do 'new' work, rather than trying to exactly reproduce existing work, then as Steve suggests the best thing to do is use the current version of R and associated Bioconductor packages, as described at http://bioconductor.org/install/ Martin > Tulay AkalResearch Assistant Middle East Technical University, > Turkey [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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