[BioC] PDNN compatibility with RAE230A

Jordi Altirriba Gutiérrez altirriba at hotmail.com
Fri Mar 4 16:22:12 CET 2005

I have installed your software PerfectMatch and I have been trying to run it 
(windows version), but I am working with Affymetrix microarrays RAE230A and 
I have not been able to find the Starting Energy parameter File for this 
Furthermore, I've tried to run the R version of Affypdnn, and I also could 
not find the file with the chiptype's parameters (.pdnn.params) for this 
Therefore, is there any way to create or obtain these files?
Finally,  I have loaded the affypdnn package in R interface, and I have 
>eset-> expresso (Data, widget=T)

In the screen has appeared all the options:
Background correction: mas, none, rma, rma2.
Normalization: constant, contrasts, invariantset, loess, qspline, quantiles, 
PM correction: mas, pmonly, substractmm, pdnn, pdnnpredict.
Expression: avgdiff, liwong, mas, medianpolish, playerout.

I know that the PMcorrection is either pdnn or pdnnpredict, but what about 
the other options? Any suggestions are more than welcome.

(R version 2.1.0, affypdnn version 1.1-0, platform Windows)
(PerfectMatch Windows version

Thank you very much for your time and help.
Yours sincerely,

Jordi Altirriba
PhD stundent
Hospital Clinic (Barcelona, Spain)

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