[BioC] Re: Suggestion for affycomp
Rafael A. Irizarry
ririzarr at jhsph.edu
Mon Jul 19 18:05:42 CEST 2004
apart from the legends given in the web-page, the paper
describing affycomp it explains each measure in more detail.
a more biologist friendly explanation is possible but requires time which
we dont necessarily have right now. contributions are welcomed.
On Mon, 19 Jul 2004, [ISO-8859-1] Hinrich Göhlmann wrote:
> 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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