Thanks, Steve and David! svm.fit<-svm(as.factor(out) ~ ., data=all_h, method="C-classification", kernel="radial", cost=bestc, gamma=bestg, cross=10, probability=TRUE)
It works this time! On Wed, May 5, 2010 at 6:24 PM, Changbin Du <changb...@gmail.com> wrote: > Thanks Steve! > > I will try and let you know how it comes. > > > > > On Wed, May 5, 2010 at 6:07 PM, Steve Lianoglou < > mailinglist.honey...@gmail.com> wrote: > >> Hi Changbin, >> >> On Wed, May 5, 2010 at 6:46 PM, Changbin Du <changb...@gmail.com> wrote: >> > svm.fit<-svm(as.factor(out) ~ ., data=all_h, method="C-classification", >> > kernel="radial", cost=bestc, gamma=bestg, cross=10) # model fitting >> > >> > svm.pred<-predict(svm.fit, hh, decision.values = TRUE, probability = >> TRUE) # >> > find the probability, but can not find. >> > >> > attr(svm.pred, "probabilities") >> > >> >> attr(svm.pred, "probabilities") >> > 1 0 >> > 1 0 0 >> > 2 0 0 >> > 3 0 0 >> > 5 0 0 >> > 6 0 0 >> > 7 0 0 >> > 8 0 0 >> > 9 0 0 >> > >> > Hi, Dear R community, >> > >> > IN my data, the out variable is the target variable (0, and 1), hh is >> the >> > new data set does not contain the out variable. I trained the model >> svm.fit >> > in training data. And want to predict the out in the new data set hh. >> > >> > WHy the probabilities are both 0 in 1 and 0 class? >> >> Look at the help for the svm function: >> >> ?svm >> >> Notice that there is a parameter in the svm function call named >> `probability` with a default value of FALSE. Try: >> >> svm.fit<-svm(as.factor(out) ~ ., data=all_h, method="C-classification", >> kernel="radial", cost=bestc, gamma=bestg, cross=10, probability=TRUE) >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: >> http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact> >> > > > > -- > Sincerely, > Changbin > -- > > > > -- Sincerely, Changbin -- Changbin Du DOE Joint Genome Institute Bldg 400 Rm 457 2800 Mitchell Dr Walnut Creet, CA 94598 Phone: 925-927-2856 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
