Machine Learning on RNA-Seq Data with MLSeq package

Question

[Mrinal.singh06]

Hi, I am working on model building on RNA-Seq data with MLSeq package and I am using classify function in MLSeq package.

my design consist of Qp_group factor that consist of High and Low variable. Day also consist of various days with different level

data.trainS4 = DESeqDataSetFromMatrix(countData = round(data.train), colData = xtr,
                                      design = ~Qp_Group+Day+Qp_Group:Day)

set.seed(2128)
ctrl.svm <- trainControl(method = "repeatedcv", number = 5, repeats = 1)

# Support vector machines with radial basis function kernel
fit.svm <- classify(data = data.trainS4, method = "svmRadial",
                    preProcessing = "deseq-vst", ref = "T", tuneLength = 10,
                    control = ctrl.svm)

On Running the classify function, I am getting the below error.

> set.seed(2128)
> ctrl.svm <- trainControl(method = "repeatedcv", number = 5, repeats = 1)
> # Support vector machines with radial basis function kernel
> fit.svm <- classify(data = data.trainS4, method = "svmRadial",
+                     preProcessing = "deseq-vst", ref = "T", tuneLength = 10,
+                     control = ctrl.svm)
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in `[.default`(data, , positive) : subscript out of bounds