On Thu, Oct 27, 2011 at 8:58 AM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

>  I am looking for a canned and validated
> function based on SQN that can be applied as easily rma that could perhaps
> yield  differentially expressed
> genes for a set of arrays where rma did not.


Wouldn't you be concerned about the trade-off between sensitivity and
specificity if the only thing that distinguished DE results from non-DE
results was the method?  It seems a bit much to put such faith in
methodology when biology is inherently complex.  "Validation" usually
consists of a handful of scenarios that the authors could think of.

I am not confident of my ability to develop
> such a method. I am hoping that someone else has done so.
>

The closest I've seen to this description was in the charm package, but...
look in the code, you'll see what I mean.

Validating a new method is pretty tricky even for people who have developed
existing methods.  And of course since new methods are far less sexy than
new biology, there is a disincentive to exhaustively test all assumptions.

JMHO

-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is.John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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