runTwoLayerExtCV-methods: runTwoLayerExtCV: Method to run an external two-layers...
In Rmagpie: MicroArray Gene-expression-based Program In Error rate estimation

Description Arguments Value Methods References See Also Examples

This method run an external two-layers cross-validation according to the options stored in an object of class assessment. The concept of two-layers cross-validation has been introduced by J.X. Zhu,G.J. McLachlan, L. Ben-Tovim Jonesa, I.A.Wood in 'On selection biases with prediction rules formed from gene expression data' and by I. A. Wood, P. M. Visscher, and K. L. Mengersen in 'Classification based upon gene expression data: bias and precision of error rates' (cf. section References). This technique of cross-validation is used to determine an unbiased estimate of the best error rate (using the best size of subset for RFE-SVM, of the best threshold for NSC) when feature selection is involved.

object

Object of class assessment. Object assessment of interest

object of class assessment in which the one-layer external cross-validation has been computed, therfore, the slot resultRepeated2LayerCV is no more NULL. This methods print out the key results of the assessment, to access the full detail of the results, the user must call the method getResults.

object = "assessment": This method is only applicable on objects of class assessment.

J.X. Zhu, G.J. McLachlan, L. Ben-Tovim, I.A. Wood (2008), "On selection biases with prediction rules formed from gene expression data", Journal of Statistical Planning and Inference, 38:374-386.

I.A. Wood, P.M. Visscher, and K.L. Mengersen "Classification based upon gene expression data: bias and precision of error rates" Bioinformatics, June 1, 2007; 23(11): 1363 - 1370.

assessment, getResults, runOneLayerExtCV-methods

data('vV70genesDataset')

# assessment with RFE and SVM
myExpe <- new("assessment", dataset=vV70genes,
                   noFolds1stLayer=9,
                   noFolds2ndLayer=10,
                   classifierName="svm",
                   typeFoldCreation="original",
                   svmKernel="linear",
                   noOfRepeat=2,
                   featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))

myExpe <- runTwoLayerExtCV(myExpe)