[R] graphlets -- more

A.J. Rossini rossini at blindglobe.net
Mon Jan 12 21:00:20 CET 2004

You might check out the prada package in Bioconductor; it's designed
for a different, but similar problem (96/384 well plate assays).
It isn't released, but the code is in the Bioconductor CVS repository,
which can be viewed and retrieved over the WWW:



Terry Therneau <therneau at mayo.edu> writes:

>   I have already recieved two very helpful replies.  Let me describe the
> problem we are trying to solve more clearly -- one of the suggestions was
> along a line I'd never thought of, and I'd like to encourage more!
>    R is being used in a microarray/QC situation, in essentially a batch
> mode.  The applications that are "running the show" in terms of interacting
> with the user's terminal and the main database are constrained to a
> very particular environment, due to other reasons (ones I happen to agree
> with, it's not just politics).  This outer application "X"
> 	- interact with the user to define "what data to look at"
> 	- and what to do with it
> 	- toss off an R batch script (a few calls, to perhaps complex
> 	functions) and a bunch of data
>  	- R sends back a "blob" that X can display
> The "blob" is an html doc with tables and plots.  The graphlet part comes
> from the desire to allow the lab tech to drill down to plots that are
> always defined and present, but rarely displayed.  The main plot contains
> results from several experiments, one looks odd, so they can click on it
> to see the per-experiment results.
>   Because of environmental and speed constraints, this is not an interactive
> R session.  The graphlets package allows this type of operation with java.
> 	Terry Therneau
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rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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