[BioC] avgdiff in place of avdiff

[Rafael A. Irizarry]

it is different. using express (another function) you can use the
predefined function avgdiff. you can do this using expresso as well but
its bit more complicated. 
in any case, you wont be able to reproduce Affy's
avg diff using the included functions becuase, for example, we havent
implemented the MAS 4.0
background correction. writting your own is relatively easy.
im sure bioconducotor
would gladly welcome a contributed
function that reproduces MAS 4.0 Avg diff measure.

thanks,
-rafael

On Thu, 5 Dec 2002, [iso-8859-1] "Hölter, Tanja" wrote:

> Hello, we work with the affy package and we try to compare the results
> from bioconductor with the results from Affymetrix. 
> In the function expresso you can choose the avgdiff as summary method.
> We noticed that the function avgdiff uses the median of the probes, but
> the Affymetrix 4 Algorithmen uses a trimmed mean. In the source code
> there is a function called avdiff, which calculates the expression value
> in the same manner as Affymetrix. Why does this function is not
> implemented in the expresso? I think to take the median, as the function
> avgdiff does, is very different to the method proposed fby Affymetrix.
> 
> Tanja Hölter
> 
> 
> 
> Dipl. Statistikerin Tanja Hölter
> Institut für Medizinische Informatik,
> Biometrie und Epidemiologie
> Universitätsklinikum Essen
> D-45122 Essen
> Tel:(49)201-723-4654
> FAX: (49)201-723-5933
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>