[BioC] Re: Suggestion for affycomp

[Rafael A. Irizarry]

apart from the legends given in the web-page, the paper
describing affycomp it explains each measure in more detail. 

http://bioinformatics.oupjournals.org/cgi/content/abstract/20/3/323?ijkey=83iw8rxPSScW6&keytype=ref

a more biologist friendly explanation is possible but requires time which
we dont necessarily have right now. contributions are welcomed.

-r

On Mon, 19 Jul 2004, [ISO-8859-1] Hinrich Göhlmann wrote:

> Hi,
> 
> 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?
> 
> Cheers,
> 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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