[BioC] biobase

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Jun 28 19:44:15 CEST 2011


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 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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