[BioC] OSX location of bioconductor functions

[J.delasHeras at ed.ac.uk]

Yes, I agree it is a little annoying to have to modify existing code  
to take into account the recent renaming of some columns. So far I've  
done just that: modifying my code. However, I suppose we could just  
insert a tiny section after we apply the "offending" functions, where  
it finds the columns that have been renamed, and change them back to  
what we were used to. I intended to do that, but I haven't had the  
need yet. That should be a lot easier than reinstalling limma from  
source...

Jose

Quoting Bobby Prill <rprill at jhu.edu>:

> Can someone tell me where toptable() code resides on an OSX
> installation?
>
> I just upgraded my R and Bioconductor.  Apparently, some rows were
> renamed in toptable().  I would like to change the row called "logFC"
> back to "M".
>
> I searched my system and can not find where any of the limma
> functions are defined.  Limma seems to be installed in:
>
> /Library/Frameworks/R.framework/Versions/2.4/Resources/library/limma/
>
> However I do not see any actual functions defined there.
>
> I installed using the command:  getBioC().  Perhaps that installed
> "binary" rather than "source" version of limma?
>
> I don't want to create a new function called my.toptable().  I just
> want all of my scripts to simply work again with a single edit of the
> true toptable().
>
> 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."
>
> I appreciate the help.  This is a great user community.
>
> - Bobby
>
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-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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