Dear Bioconductor users, There is a error message when I run the following code. It is used to load microarray data and use the top 1000 genes for training svm to classify test set . > library(e1071) Loading required package: class > f=read.table("F:\\lab\\microarray analysis\\VEH LPS\\exprs.txt", sep="\t",header=FALSE,col.names=c("Gene","VEH","VEH","VEH","VEH","VEH" ,"LPS","LPS","LPS","LPS","LPS")) > tf=t(f) > colnames(tf)=tf[1,] > tf=tf[-1,] > tf=as.data.frame(tf) > array <- apply(tf[,2:24928],c(1,2),as.numeric) > label <- as.factor(tf$ENTREZGENE) > > n <- nrow(array) #get sample number > permutation <- sample(1:n) > array.perm <- array[permutation,] # random permutation of samples > label.perm <- label[permutation] # same permutation of labels > > k <- 5 #set cross validation steps > > for (i in 1:k){ + win <- round(n/k) # size of window + cv <- ((i-1)*win+1):min(n,i*win) # move window + + CV.label.test <- label.perm[cv] + CV.label.train <- label.perm[-cv] + + CV.train.neg.num <- nrow(as.data.frame(CV.label.train[CV.label.train=="VEH"])) + CV.train.pos.num <- nrow(as.data.frame(CV.label.train[CV.label.train=="LPS"])) + CV.train.num <- CV.train.pos.num+CV.train.neg.num + + CV.test <- array.perm[cv,] # samples within window + CV.train <- array.perm[-cv,] # samples outside window + + CV.train.pos <- as.data.frame(CV.train)[as.data.frame(CV.label.train)=="LPS",] # matrix of positive samples + CV.train.pos.mean <- apply(CV.train.pos,2,mean) # compute mean of each column (gene) + CV.train.pos.var <- apply(CV.train.pos,2,var) # compute variance of each column (gene) + + CV.train.neg <- as.data.frame(CV.train)[as.data.frame(CV.label.train)=="VEH",] # matrix of positive samples + CV.train.neg.mean <- apply(CV.train.neg,2,mean) # compute mean of each column (gene) + CV.train.neg.var <- apply(CV.train.neg,2,var) + + tscore <-(abs(CV.train.pos.mean-CV.train.neg.mean)/sqrt((CV.train.pos.num-1)* CV.train.pos.var+(CV.train.neg.num-1)*CV.train.neg.var))*sqrt(CV.train .pos.num*CV.train.neg.num*(CV.train.num-2)/CV.train.num) + index <- order(tscore, decreasing=TRUE) + CV.train=CV.train[,index[1:100]] + + svm.train<-svm(CV.train, CV.label.train, type="C-classification", kernel="linear", cross=5, scale=TRUE) + } > pred<-predict(svm.train,CV.test) Error in scale.default(newdata[, object$scaled, drop = FALSE], center = object$x.scale$"scaled:center", : length of 'center' must equal the number of columns of 'x' I wonder what is the reason for such kind of error. > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=Chinese_People's Republic of China.936 [2] LC_CTYPE=Chinese_People's Republic of China.936 [3] LC_MONETARY=Chinese_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] e1071_1.5-24 class_7.3-2 Thanks a lot! -- Best Regards, Zhe Liu [[alternative HTML version deleted]]