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]]
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
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