[BioC] Request for installation of software R2.13/Biconductor 2.8

[Dan Tenenbaum]

Hi Mayur,

----- Original Message -----
> From: "Mayur Doke" <mdoke001 at fiu.edu>
> To: bioconductor at r-project.org
> Sent: Wednesday, February 26, 2014 12:35:58 PM
> Subject: [BioC] Request for installation of software R2.13/Biconductor 2.8
> 
> Dear Sir/Madam,
> 
> I am Mayur Doke persuing PhD in Public Health from Florida
> International
> University. I have read  research article on Idiopathic and heritable
> PAH
> perturb common molecular pathways, correlated with increased MSX1
> Expression which Published in Journal of Pulmonary Circulation of
> july-sept
> 2011 issue. In this research paper, researchers have mentioned that
> the
> open source software, R2.13/Biconductor 2.8 utilized for microarray
> analysis.
> 
> The issue is I am not getting the software from the link in website
> which
> you have provided. So could you please guide me in order to install
> the
> above mentioned software.
> 

If you want to reproduce exactly the analysis in the paper, you should use 
R-2.13 and Bioconductor 2.8. However, be aware that reproducibility is the ONLY reason to use older versions. 
For any other reasons you should use current versions of R (3.0.2) and Bioconductor (2.13).

If you do want to install the older versions, all you have to do is install R 2.13 from http://cran.r-project.org/. The exact link varies depending on your OS. 

For windows:
http://cran.r-project.org/bin/windows/base/old/

For Mac:
http://cran.r-project.org/bin/macosx/old/

For Linux and other Unices, install a source tarball here:
http://cran.r-project.org/src/base/

Once you have done that, start R and type:

source("http://bioconductor.org/biocLite.R")

This will allow you to automatically install the appropriate version of Bioconductor packages using the biocLite() command. 


For example, to install Biobase:

biocLite("Biobase")

The package pages of Bioconductor version 2.8 are visible here:

http://www.bioconductor.org/packages/2.8/BiocViews.html#___Software

But you should only use this page to read about the packages. You should install them as I've described above (and as mentioned on each package page).

Thanks,
Dan



> Thanking you,
> 
> Mayur Doke
> 
> 	[[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
>