[BioC] problem installing the affy package

[James W. MacDonald]

Hi Martin,

Martin O'Gorman wrote:
> Hi there, I have just installed the "affy" package from bioconductor
> by downloading the .zip file for windows and extracting to
> ..\R\R-2.3.1\library\ ,ie the directory where all my R packages live.
> However, I can't seem to open the package, getting the following
> error message.
> 
>> library(affy)
> Error in library(affy) : there is no package called 'affy'
> 
> I have followed the same procedure for affyio without any problems.
> Am I doing something wrong?

Yep. You are doing things about as wrong as you possibly could (where 
did you get this idea?).

You really shouldn't be downloading things directly, and you certainly 
shouldn't just be unzipping things in library directories. The preferred 
method is to use biocLite() to get things, as this function will a.) 
install things correctly, b.) get the correct version for the version of 
R you are using, and c.) get all other packages that the package you 
want depends on.

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

BTW, R-2.3.1 is pretty old; you should probably upgrade to 2.5.1 while 
you are at it.

Best,

Jim


> 
> thanks Martin
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623