How to perform classification of Differentially expressed genes using Random Forest?

Question

[gurudeeb99]

Dear All,

I try to implement deep learning for cancer biomarkers. I read your article ( Machine Learning For Cancer Classification - Part 2 - Building A Random Forest Classifier ), it very useful to me, but I have encountered more errors.

In my study, the DEGs were extracted from the meta-analysis. Then, I performed 10 fold cross validation, its fine. In addition, I try to classify the data using RF. I performed RF as per example scripts. However, I encountered an error as follows

for(i in cols){
+   DataFrame[,i]=as.factor(DataFrame[,i])
+ }

Error: Can't use matrix or array for column indexing

This is my model script

library (readxl)
library(randomForest)
set.seed (123)
DataFrame <-ADSC_RF 
View (DataFrame)
structure (DataFrame)
dim(DataFrame)
head(DataFrame,3)
summary(DataFrame)
apply(DataFrame,2,function (x) length (unique(x)))
cols<-c("Target")
for(i in cols){
  DataFrame[,i]=as.factor(DataFrame[,i])
}
str(DataFrame)
library (caTools)
ind = sample.split (Y=DataFrame$Target,SplitRatio = 0.7)
trainDF<-DataFrame[ind,]
testDF<-DataFrame[!ind,]
modelRandom<-randomForest(Target~.,data = trainDF,mtry=3,ntree=20)
Yes
modelRandom
importance(modelRandom)
varImpPlot(modelRandom)
PredictionWithClass<-predict(modelRandom, testDF, type = 'class')
PredictionWithClass
t<-table(predictions=PredictionWithClass, actual=testDF$Target)
t
sum (diag(t))/sum (t)
library(pROC)
PredictionsWithProbs<-predict(modelRandom, testDF, type = 'prob')
PredictionsWithProbs
auc<-auc(testDF$Target, PredictionsWithProbs[,2])
auc
plot(roc(testDF$Target,PredictionsWithProbs[,2]))
bestmtry<-tuneRF(trainDF, trainDF$Target, ntreeTry=200, stepFactor = 1.5, improve =0.01, trace =T, plot =T)

This is my source file,

A               B              C              D             E              F                G                H    I Target
3886.10 1566.40 3336.30 269.77  2386.10 826.20  2728.20 4707.10 3462.10 1
845.29  783.52  909.08  111.97  888.53  167.00  728.97  1111.20 994.12  1
52.43   57.13   1740.30 269.53  1595.60 454.48  1296.00 1528.30 1312.40 1
521.30  170.27  2205.00 208.64  2141.10 567.01  1711.40 1928.50 1692.70 1

I feel, I have to change the column name and include the expression library. But, I am not sure.

Can you help me to fix this issue?

Answer 1

[Devon Ryan]

That bit of the code makes no sense. Replace this:

DataFrame[,i]=as.factor(DataFrame[,i])

with this:

DataFrame[[i]]=as.factor(DataFrame[[i]])

Alternatively, remove the whole for loop and just use DataFrame$Target = as.factor(DataFrame$Target).

[gurudeeb99]

Dear Ryan,

Thanks a lot. It's working now with the comment "DataFrame$Target = as.factor(DataFrame$Target)".