Question: Feature(Gene) selection using R Caret package: Error in seeds[[num_rs + 1L]] : subscript out of bounds
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gravatar for The
4.0 years ago by
The160
United States
The160 wrote:

Hello All,

I've a dataset of six samples and 1530 genes(features) and wish to know the the importance of features. I'm trying to use the "Rank Features By Importance" as mentioned in Feature Selection with the Caret R Package.

I'm using the following code:

rm(list=ls())
set.seed(12345)
library(mlbench)
library(caret)
options(error=utils::recover)

#Pastebin link for Data: http://pastebin.com/raw/cg0Kiueq
mydata.df <- read.table("data.PasteBin.txt", header=TRUE,sep="\t",stringsAsFactors=TRUE)
dim(mydata.df)

lvq.control <- trainControl(method="LOOCV")
lvq.model <- train(ID~., data=mydata.df, method="lvq", trControl=lvq.control ) #FAILS

importance <- varImp(lvq.model, scale=FALSE)
print(importance)
plot(importance)

The data can be downloaded from the following Pastebin LINK

The program fails to execute with the following error and debug messages:

Error in seeds[[num_rs + 1L]] : subscript out of bounds
1: train(ID ~ ., data = mydata.df, method = "lvq", trControl = lvq.control)
2: train.formula(ID ~ ., data = mydata.df, method = "lvq", trControl = lvq.con
3: train(x, y, weights = w, ...)
4: train.default(x, y, weights = w, ...)

I've read from multiple sources that unless the response variable is of class factor Caret issues error like this. However, my response variable('ID') is indeed a factor

> str(mydata.df$ID)
 Factor w/ 2 levels "NONRC","RC": 2 2 1 1 2 1
The detail of my version of R and Caret are as follows:

> packageVersion("caret")
[1] ‘6.0.70’
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Can someone please suggest any remedy?

Thanks in advance

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by The160

I have the same problem,did you find any solution?

ADD REPLYlink written 2.3 years ago by h72ghorashi0
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