[BioC] OSX location of bioconductor functions

[James W. MacDonald]

Bobby Prill wrote:
> As an aside, I can't imagine why the column names in ANY function  
> would be changed.  These column names are essentially the external  
> interface to the function.  It seems like a very bad design decision  
> to just one day change "M" to "logFC."

What has been changed is the output of a function (which is _not_ the 
external interface to the function), and IIRC the change was made to 
better reflect what the column contained.

The version of limma that had the columns labeled M and A still does 
exist, and a simple downgrade to R-2.3.1 and a biocLite() will get you 
there.

Anyway, I'm not sure I follow your logic. Are you saying that the output 
of _all_ functions once written should be inviolate? So no change, no 
matter how incremental is allowed? Personally, I couldn't disagree more 
with this stance. You cannot improve things if you are not allowed to 
make changes to both the API and the output.


Best,

Jim

-- 
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


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