[BioC] Suggestion for affycomp

Hinrich Göhlmann hgoehlma at gmx.de
Mon Jul 12 08:47:34 CEST 2004

Good morning,

I have a suggestion for affycomp and it's accompanying web site at

I very much like the idea to check how the different algorithms perform 
but I would even more appreciate a biologist-compatible interpretation 
of the comparison table (low or no stats!). What I have in mind is 
something like:
(1) define all the different approaches that people could be interested 
in from a statistical point of view (Example: I am interested in a best 
possible accuracy of fold change estimation at all signal levels. For 
this application, score components 4, 7, and 13 are most important (I 
don't know!). OR: I would like to have the highest possible precision 
for the signal levels. For this application score components 3, 6, 8, 
and 11 are most important. OR: I need best possible precision for low 
expressed genes. For this components x, y, and z are most important. And 
so on...
(2) make a table with those applications and give the 2 or three best 
suitable algorithms for those applications.

By openly defining those applications at such a web site, we can get a 
discussion going on what components most people agree on per application 
and can secondly make practical use of the data that gets collected.

hinrich   d8-)

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