[BioC] biobase

[Steve Lianoglou]

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