[BioC] biobase

[Martin Morgan]

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]]
>
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