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

[James W. MacDonald]

On 1/28/2011 3:23 PM, James Carman wrote:
> 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?

Not so much that either book is obsolete. Maybe Amazon has both together 
for a good deal ;-D



-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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