(s)PLS-DA

PLS Discriminat Anlysis (PLS-DA)

Although Partial Least Squares was not originally designed for classification and discrimination prob- lems, it has often been used for that purpose (Nguyen and Rocke, 2002; Tan et al., 2004). The response matrix Y is qualitative and is internally recoded as a dummy block matrix that records the membership of each observation, i.e. each of the response categories are coded via an indicator variable. The PLS regression (now PLS-DA) is then run as if Y was a continuous matrix. Note that this might be wrong from a theoretical point of view, however, it has been previously shown that this works well in practice.

  • PLS-Discriminant Analysis (PLS-DA) is a linear model which performs a classification task and is able to predict the class of new samples (Barker and Rayens, 2003).

  • The sparse variant sparse PLS-DA (sPLS-DA) enables the selection of the most predictive or discriminative features in the data that help classify the samples (Lê Cao et al., 2011).

sparse PLS Discriminat Analysis (sPLS-DA)

sPLS-DA performs variable selection and classification in a one step procedure. sPLS-DA is a special case of sparse PLS to allow variable selection, except that this time, the variables are only selected in the X data set and in a supervised framework, i.e. we are selecting the X-variables with respect to different categories of the samples.

Usage in mixOmics

(s)PLS-DA is implemented in mixOmics via the functions plsda() and splsda() as displayed below. For both plsda and splsda, we strongly advise to work with a training and a testing set.

PLS-DA

Variable selection

Similar to a PLS-regression mode, the tuning parameters include the number of dimensions or components ncomp. We can rely on the estimation of the classification error rate using leave-one-out or cross-validation. We use the function perf() to evaluate a PLS-DA model and predict().

library(mixOmics)
data(liver.toxicity)
X <- as.matrix(liver.toxicity$gene)
Y <- as.factor(liver.toxicity$treatment[, 4])             

## PLS-DA function
result <- plsda(X, Y, ncomp = 3) # where ncomp is the number of components wanted

sPLS-DA

Tuning sPLS-DA

We use the function tune.splsda() to select the parameters including the number of components/dimensions, ncomp, and the number of variables to choose in the X data set, keepX.

# grid of possible keepX values that will be tested for comp 1 and comp 2
list.keepX <- c(1:10,  seq(20, 100, 10))
# to speed up computation in this example we choose 5 folds repeated 10 times:
tune.splsda.srbct <- tune.splsda(X, Y, ncomp = 5, validation = 'Mfold', folds = 5, 
                           progressBar = FALSE, dist = 'mahalanobis.dist',
                           test.keepX = list.keepX, nrepeat = 10) #nrepeat 50-100
## sPLS-DA function
result <- splsda(X, Y, ncomp = 3, keepX = c(10, 10, 10)) # where keepX is the number of variables selected for each components

With (s)PLS-DA, the classes of new samples or observations can be predicted in the model by using thepredict function. This is an example to perform 3-fold cross-validation. Normally 10-fold cross-validation should be performed several times and the results should be averaged to get a better estimation of the generalization performance:

data(liver.toxicity)
X <- as.matrix(liver.toxicity$gene)
Y <- as.factor(liver.toxicity$treatment[, 4]) # Y is a factor, we chose it as the time points of necropsy
i <- 1
samp <- sample(1:3, nrow(X), replace = TRUE) # Creation of a list of the same size as X containing 1, 2 or 3

test <- which(samp == i) # Search which column in samp has a value of 1
train <- setdiff(1:nrow(X), test) # Keeping the column that are not in test

## For PLS-DA
plsda.train <- plsda(X[train, ], Y[train], ncomp = 3)
test.predict <- predict(plsda.train, X[test, ], method = "max.dist")

## For sPLS-DA
splsda.train <- splsda(X[train, ], Y[train], ncomp = 3, keepX = c(10, 10, 10))
test.predict <- predict(splsda.train, X[test, ], method = "max.dist")

See Case Study: sPLS-DA srbct for more details and plotting options.

Reference

In addintion to references form (s)PLS.

Pérez-Enciso, M. and Tenenhaus, M., 2003. Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Human genetics, 112(5-6), pp.581-592.

Nguyen, D.V. and Rocke, D.M., 2002. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics, 18(1), pp.39-50.

Lê Cao, K.A., Boitard, S. and Besse, P., 2011. Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC bioinformatics, 12(1), p.253