I am trying to find class-specific features in a gene expression data set using sPLS-DA model. After tuning for the optimal number of components and variables, I built the final sPLS-DA model using the below mentioned piece of code:
splsda.res.final = mixOmics::splsda(X = training_data, Y = response.variable.training, ncomp = 6, keepX = c(743, 124, 372, 268, 619, 248), mode = “regression”, scale = FALSE, tol = 1e-06, max.iter = 100, near.zero.var = FALSE, all.outputs = TRUE);
>splsda.res.final sPLS-DA (regression mode) with 6 sPLS-DA components. You entered data X of dimensions: 380 12368 You entered data Y with 5 classes. Selection of       variables on each of the sPLS-DA components on the X data set. No Y variables can be selected.
I thought there are 743 variables in component 1, but when I used selectVar(), I got 995 variables.
length(mixOmics::selectVar(object = splsda.res.final, comp = 1)$name)
Can someone help me to understand this observation?