Dear list, According to the example given in "compare" help page for CMA package, I've executed the following code: ### compare the performance of several discriminant analysis methods ### for the Khan dataset: data(khan) khanX <- as.matrix(khan[,-1]) khanY <- khan[,1] set.seed(27611) fiveCV10iter <- GenerateLearningsets(y=khanY, method = "CV", fold = 5, niter = 2, strat = TRUE) ### candidate methods: DLDA, LDA, QDA, pls_LDA, sclda class_dlda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = dldaCMA) ### peform GeneSlection for LDA, FDA, QDA (using F-Tests): genesel_da <- GeneSelection(X=khanX, y=khanY, learningsets = fiveCV10iter, method = "f.test") ### class_lda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = ldaCMA, genesel= genesel_da, nbgene = 10) class_qda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = qdaCMA, genesel = genesel_da, nbgene = 2) ### We now make a comparison concerning the performance (sev. measures): ### first, collect in a list: dalike <- list(class_dlda, class_lda, class_qda) ### use pre-defined compare function: comparison <- compare(dalike, plot = TRUE, measure = c("misclassification", "brier score", "average probability")) print(comparison) ## End(Not run) Everyhing is OK. However, if I add a new classification method using SVM like this: class_svm<- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = svmCMA, genesel = genesel_da, nbgene = 2,kernel="radial") classifierlist <- list(class_dlda, class_lda, class_qda, class_svm) par(mfrow = c(4, 1)) comparison <- compare(classifierlist, plot = TRUE, measure = c("misclassification", "brier score", "average probability")) I got the following error in compare function: Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : contrasts can be applied only to factors with 2 or more levels Any tips? Thanks in advance, Javier > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MASS_7.3-3 class_7.3-1 CMA_1.4.1 Biobase_2.6.0 e1071_1.5-20 loaded via a namespace (and not attached): [1] tools_2.10.0