[BioC] Problem with affy mas5 on Linux but not Windows...

[James Carman]

On Fri, Jan 28, 2011 at 3:01 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
> You want to follow the instructions for updating packages, not
> installing a particular one; likely you have a Frankenstein system at
> the moment. In a new R
>
> source('http://bioconductor.org/biocLite.R')
> update.packages(repos=biocinstallRepos(), ask=FALSE)
>

I went with this approach, since this is what the Bioconductor folks
have on their site.

> or a recently learned (for me) and probably better approach
>
> options(repos=c(CRAN="http://cran.fhrcr.org"))
> setRepositories()  ## select CRAN and all BioC
> old.packages()  ## to see what you are saving yourself from...
> update.packages(ask=FALSE)
>

This looked a bit scary to me with the hard-coded server name in
there, so I went with the other way. :)

> In terms of books from a developer perspective (rather than 'using R' or
> 'bioinformatic analysis') I'm partial to Chambers' Software for Data
> Analysis and Gentleman's R Programming for Bioinformatics.
>

Cool, thanks!  These books are a bit old.  Is there any reason to
worry about that?  Has the information become obsolete at all?  Has R
changed that much in the past 2-3 years?