Leukemia AML ALL classification
Valerie Monbet
19/8/2017
Data loading
Read Leukemia gene expression dataset
gene = read.csv("https://perso.univ-rennes1.fr/valerie.monbet/DATA/data_set_ALL_AML_train.csv",header=TRUE,sep="\t")
ncol(gene)## [1] 78nrow(gene)## [1] 7129As usual, this gene expression dataset is stored with the sample (patients) in columns and the gene in rows. For the statistical analysis, a transposition is needed.
X = t(gene[,seq(3,ncol(gene),by=2)])
Y = as.factor(c(rep(1,27),rep(2,11))) # class label (2 = AML, 1 = ALL)K nearest neighbors ===================================
library(class)
library(pROC)## Type 'citation("pROC")' for a citation.##
## Attaching package: 'pROC'## The following objects are masked from 'package:stats':
##
## cov, smooth, varSeed = "1223"
set.seed(Seed)
n = nrow(X) ; n.train = round(n*2/3)
data = data.frame(cbind(X,Y))
data$Y = as.factor(data$Y)
set.seed(Seed)
test <- prob1 <- prob3 <- prob5 <- prob7<- prob9 <-NULL
B = 100
for (b in 1:B){
i.TRAIN = sample(1:n,n.train) ;
i.TEST = setdiff(1:n,i.TRAIN) ;
test = c(test,i.TEST)
rho = NULL
for (k in 1:ncol(X)){
rho[k] = abs(cor(X[i.TRAIN,k],as.numeric(Y[i.TRAIN])))
}
w = which(abs(rho)>.5)
TRAIN = data[i.TRAIN,c(w,dim(data)[2])]
TEST = data[i.TEST,c(w,dim(data)[2])]
knn1 = knn(TRAIN[,-(length(w)+1)],TEST[,-(length(w)+1)],TRAIN$Y,k=1,prob=TRUE)
prob1 = c(prob1,attributes(knn1)$prob)
knn3 = knn(TRAIN[,-(length(w)+1)],TEST[,-(length(w)+1)],TRAIN$Y,k=3,prob=TRUE)
prob3 = c(prob3,attributes(knn3)$prob)
knn5 = knn(TRAIN[,-(length(w)+1)],TEST[,-(length(w)+1)],TRAIN$Y,k=5,prob=TRUE)
prob5 = c(prob5,attributes(knn5)$prob)
knn7 = knn(TRAIN[,-(length(w)+1)],TEST[,-(length(w)+1)],TRAIN$Y,k=7,prob=TRUE)
prob7 = c(prob7,attributes(knn7)$prob)
knn9 = knn(TRAIN[,-(length(w)+1)],TEST[,-(length(w)+1)],TRAIN$Y,k=9,prob=TRUE)
prob9 = c(prob9,attributes(knn7)$prob)
}
Ytest = data[test,dim(data)[2]]
Ychar=NULL
Ychar[Ytest==levels(Ytest)[1]] = "AML"
Ychar[Ytest=="2"] = "ALL"
boxplot(prob7~Ychar,ylab="Predicted probabilities")
ROC curve
roc5 = roc(data[test,dim(data)[2]],prob5)
plot(roc5)
roc9 = roc(data[test,dim(data)[2]],prob9)
plot(roc9,add=TRUE,col="gray")
roc7 = roc(data[test,dim(data)[2]],prob7)
plot(roc7,add=TRUE,col="blue",lty=2)
roc7$auc## Area under the curve: 0.8869legend("bottomright",legend=c("k=5","k=7","k=9"),lty=c(1,2,1),col=c("black","blue","gray"))
## Decision trees
library(rpart)
n.train = 34
set.seed(Seed)
test <- pred <-NULL
B = 100
for (b in 1:B){
i.TRAIN = sample(1:n,n.train) ;
i.TEST = setdiff(1:n,i.TRAIN) ;
test = c(test,i.TEST)
rho = NULL
for (k in 1:ncol(X)){
rho[k] = abs(cor(X[i.TRAIN,k],as.numeric(Y[i.TRAIN])))
}
w = which(abs(rho)>.7)
TRAIN = data.frame(X=scale(data[i.TRAIN,w]),Y=data$Y[i.TRAIN])
Xtest = scale(data[i.TEST,w],center=apply(data[i.TRAIN,w],2,mean),scale=apply(data[i.TRAIN,w],2,sd))
TEST = data.frame(X=Xtest,Y=data$Y[i.TEST])
rp = rpart(Y~.,data=TRAIN,control=rpart.control(minsplit = 4,cp=0.0001))
pred = c(pred,predict(rp,TEST,type="prob")[,1])
}
roc.rp = roc(data[test,dim(data)[2]],pred)
plot(roc.rp)
roc.rp$auc## Area under the curve: 0.8855grid()
Linear discriminant analysis
library(MASS)
n.train = 34
set.seed(Seed)
test <- pred <-NULL
B = 100
for (b in 1:B){
i.TRAIN = sample(1:n,n.train) ;
i.TEST = setdiff(1:n,i.TRAIN) ;
test = c(test,i.TEST)
rho = NULL
for (k in 1:ncol(X)){
rho[k] = abs(cor(X[i.TRAIN,k],as.numeric(Y[i.TRAIN])))
}
w = which(abs(rho)>.5)
TRAIN = data.frame(X=scale(data[i.TRAIN,w]),Y=data$Y[i.TRAIN])
Xtest = scale(data[i.TEST,w],center=apply(data[i.TRAIN,w],2,mean),scale=apply(data[i.TRAIN,w],2,sd))
TEST = data.frame(X=Xtest,Y=data$Y[i.TEST])
mod.lda = lda(Y~.,data = TRAIN)
pred = c(pred,predict(mod.lda,TEST)$posterior[,1])
}## Warning in lda.default(x, grouping, ...): variables are collinear
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## Warning in lda.default(x, grouping, ...): variables are collinear
## Warning in lda.default(x, grouping, ...): variables are collinear
## Warning in lda.default(x, grouping, ...): variables are collinear
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## Warning in lda.default(x, grouping, ...): variables are collinear
## Warning in lda.default(x, grouping, ...): variables are collinear
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## Warning in lda.default(x, grouping, ...): variables are collinear
## Warning in lda.default(x, grouping, ...): variables are collinearroc.lda = roc(data[test,dim(data)[2]],pred)
plot(roc.lda)
grid()
Logistic regression
n.train = 34
set.seed(Seed)
test <- pred <-NULL
B = 100
for (b in 1:B){
i.TRAIN = sample(1:n,n.train) ;
i.TEST = setdiff(1:n,i.TRAIN) ;
test = c(test,i.TEST)
rho = NULL
for (k in 1:ncol(X)){
rho[k] = abs(cor(X[i.TRAIN,k],as.numeric(Y[i.TRAIN])))
}
w = which(abs(rho)>.5)
TRAIN = data.frame(X=scale(data[i.TRAIN,w]),Y=data$Y[i.TRAIN])
Xtest = scale(data[i.TEST,w],center=apply(data[i.TRAIN,w],2,mean),scale=apply(data[i.TRAIN,w],2,sd))
TEST = data.frame(X=Xtest,Y=data$Y[i.TEST])
mod.lr = glm(Y~.,data = TRAIN, family="binomial")
pred = c(pred,predict(mod.lr,TEST,type="response"))
}## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
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## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleading
## Warning in predict.lm(object, newdata, se.fit, scale = 1, type =
## ifelse(type == : prediction from a rank-deficient fit may be misleadingroc.lr = roc(data[test,dim(data)[2]],pred)
plot(roc.lr)
grid()
Logistic regression + LASSO
library(glmnet)## Loading required package: Matrix## Loading required package: foreach## Loaded glmnet 2.0-5##
## Attaching package: 'glmnet'## The following object is masked from 'package:pROC':
##
## aucn.train = 34
set.seed(Seed)
test <- pred <-NULL
B = 100
for (b in 1:B){
i.TRAIN = sample(1:n,n.train) ;
i.TEST = setdiff(1:n,i.TRAIN) ;
test = c(test,i.TEST)
rho = NULL
for (k in 1:ncol(X)){
rho[k] = abs(cor(X[i.TRAIN,k],as.numeric(Y[i.TRAIN])))
}
w = which(abs(rho)>.5)
TRAIN = data.frame(X=scale(data[i.TRAIN,w]),Y=data$Y[i.TRAIN])
Xtest = scale(data[i.TEST,w],center=apply(data[i.TRAIN,w],2,mean),scale=apply(data[i.TRAIN,w],2,sd))
TEST = data.frame(X=Xtest,Y=data$Y[i.TEST])
cv = cv.glmnet(as.matrix(TRAIN[,-dim(TRAIN)[2]]),TRAIN$Y,family="binomial",type.measure="auc",nfolds=3)
mod.lr = glmnet(as.matrix(TRAIN[,-dim(TRAIN)[2]]),TRAIN$Y,lambda=cv$lambda.1se,family="binomial")
pred = c(pred,predict(mod.lr,as.matrix(TEST[,-dim(TRAIN)[2]]),type="response"))
}## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## ground
## Warning in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
## one multinomial or binomial class has fewer than 8 observations; dangerous
## groundroc.lr = roc(data[test,dim(data)[2]],pred)
plot(roc.lr)
grid()