Soma Saha wrote: > Hi! > > I got the following runtime error when I tried to use svm method with > stepclass. > > Error in "colnames<-"(`*tmp*`, value = c("0", "1")) : > attempt to set colnames on object with less than two dimensions > > I repeated the same sequence of statements but this time I used the > classification function used in the example, i.e., "lda" and it worked > fine but I got the same error when I tried randomForest. > > As the same script worked with a different classification function, I am > wondering if stepclass works with svm and randomForest. > > I using R version 2.0.1 on a Linux machine. I am including the R script I > used below. > > I would be grateful for any suggestion on how to make stepclass work with > these classification functions. > > I would also like to make stepclass work with knn but knn does not have a > 'predict' method, which is a requirement for a classification method to > work with stepclass. Is there any way to get around this? > > Thanks, > Soma > > > > library("e1071") > library("randomForest") > library("klaR") > > td <- read.table("dgdata1.txt", header=TRUE, sep=",") > dgenes <- subset(td, dg == 1, select = dg:eg) > ndgenes <- subset(td, dg == 0, select = dg:eg) > n1 <- nrow(dgenes) > n2 <- nrow(ndgenes) > ndgrows <- 1:n2 > selrows <- sample(ndgrows) > sndgenes <- ndgenes[selrows[1:n1],] > > train <- rbind(dgenes, sndgenes) > attach(train) > traind <- subset(train, select = -dg) > trainr <- factor(dg) > detach(train) > > sc_res <- stepclass(traind, trainr, "svm", direction = "forward", > criterion = "AC", fold = 10)
Looks like predict.svm does not always return "probabilities" in all cases, hence cannot be used in your case, I guess. svmlight (interface in in packages klaR) will do, though. You also might want to use sknn() (also package klaR), since it has a predict method rather than knn(). For randomForest, we will enhance stepclass() to support it in future. Uwe Ligges > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html