I write down a script to calculate correlation to remove highly correlated variable before feature selection and ML model building.
library('caret')
df1 = read.csv("stack.csv")
print (df1)
GA PN PC MBP GR AP
1 0.033 6.652 6.681 0.194 0.874 3.177
2 0.034 9.039 6.224 0.194 1.137 3.400
3 0.035 10.936 10.304 1.015 0.911 4.900
4 0.022 10.110 9.603 1.374 0.848 4.566
5 0.035 2.963 17.156 0.599 0.823 9.406
6 0.033 10.872 10.244 1.015 0.574 4.871
7 0.035 21.694 22.389 1.015 0.859 9.259
8 0.035 10.936 10.304 1.015 0.911 4.500
df2 = cor(df1)
hc = findCorrelation(df2, cutoff=0.3) # putt any value as a "cutoff"
hc = sort(hc)
reduced_Data = df1[,-c(hc)]
print (reduced_Data)
GA PN GR AP
1 0.033 6.652 0.874 3.177
2 0.034 9.039 1.137 3.400
3 0.035 10.936 0.911 4.900
4 0.022 10.110 0.848 4.566
5 0.035 2.963 0.823 9.406
6 0.033 10.872 0.574 4.871
7 0.035 21.694 0.859 9.259
8 0.035 10.936 0.911 4.500
My question is that to remove the correlated feature should I used normalized data.
preObj <- preProcess(nd[,2:(x-1) ], method=c("center", "scale"))
normalized_Data <- predict(preObj, nd[,2:(x-1)])
or I can use the raw data to calculate the correlation.
Thank you.