[BioC] Re: Suggestion for affycomp

Hinrich Göhlmann hgoehlma at gmx.de
Mon Jul 19 10:22:02 CEST 2004


hmmm...   was my question/suggestion that weird or not understandable 
(English is not my native language...) or is there simply no need for 
such an overview table?

hinrich    d8-)

Hinrich Göhlmann wrote:
> Good morning,
> I have a suggestion for affycomp and it's accompanying web site at
> http://affycomp.biostat.jhsph.edu/AFFY2/TABLES.hgu/0.html
> 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.
> Cheers,
> hinrich   d8-)

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