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zhangyuqing / simulatorZ

simulates collections of independent genomic data sets, and performs within- and across-study training and validation with predicting algorithms
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Reference #4

Closed lgatto closed 9 years ago

lgatto commented 9 years ago

Is there a reference/paper that can be used to refer to this package, or another published material that uses simulatorZ? cc @lwaldron

lwaldron commented 9 years ago

Hi @lgatto - the package itself isn't published yet, but the method was described in this paper which you can cite in the meantime:

Bernau C, Riester M, Boulesteix A-L, Parmigiani G, Huttenhower C, Waldron L, Trippa L: Cross-study validation for the assessment of prediction algorithms. Bioinformatics 2014, 30:i105–12.

@zhangyuqing - let's submit soon!

lgatto commented 9 years ago

Thanks @lwaldron.

lwaldron commented 9 years ago

@lgatto , it occurred to me that I didn't ask what you wanted to cite it for. The above paper describes the simulation of independent studies. The following paper describes the plus/minus or mas-o-menos discrimination method that the rowCoxTests() function might be used for:

Zhao SD, Parmigiani G, Huttenhower C, Waldron L: Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics 2014, 30:3062–3069.

lgatto commented 9 years ago

@lwaldron It's for a short manuscript about testing and validation of computational methods, in particular about data simulation.

lwaldron commented 9 years ago

@lgatto Neat! Looking forward to seeing it in print.