[BioC] installation of affycoretools

[James W. MacDonald]

James Anderson wrote:
> Dear list,
> 
> Is there any specific requirement for installation of affycoretools? like the version of R, etc. I am trying to install affycoretools, but there is always some error msg like:
> 
> Error: package 'GO.db' required by 'GOstats' could not be found.
> After I fix the above error, there is some new error:
> 
> Error: package 'DBI' required by 'AnnotationDbi' could not be found
> I fix this one there is some new one and seems that it will never end. 

This question is astonishingly similar to a question of yours that was 
answered just seven days ago:

https://stat.ethz.ch/pipermail/bioconductor/2007-December/020480.html
> 
> So what should I do in order to install affycoretools? 

As in the last response, and to any future question about installing 
packages -- please use biocLite() to install BioC packages. The 
dependencies for almost all of these packages are such that you will 
endure no amount of anguish by ignoring this advice and attempting to 
install packages one by one.

> In addition, the function affystart in affycoretools can be used to plot the distribution of intensity, what is the corresponding function in package affy to perform the same task? I am trying to plot the intensity distribution from two batches of data. 
> 
> Thanks a lot! Happy holidays,
> 
> James
> 
> 
> 
>        
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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
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