PDNN compatibility with RAE230A
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@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
Dear, 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 microarray. 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 array. Therefore, is there any way to create or obtain these files? Finally, I have loaded the affypdnn package in R interface, and I have written: >Data->ReadAffy() >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, quantiles.robust. 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 2.3.0.0) Thank you very much for your time and help. Yours sincerely, Jordi Altirriba PhD stundent Hospital Clinic (Barcelona, Spain)
affypdnn affypdnn • 598 views

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