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]]

