qdaCMA: Quadratic Discriminant Analysis
In chbernau/CMA: Synthesis of microarray-based classification

Description Usage Arguments Value Note Author(s) References See Also Examples

Performs a quadratic discriminant analysis under the assumption of a multivariate normal distribution in each classes without restriction concerning the covariance matrices. The function qda from the package MASS is called for computation.

For S4 method information, see qdaCMA-methods.

1	qdaCMA(X, y, f, learnind,models=FALSE, ...)

`X`	Gene expression data. Can be one of the following: A `matrix`. Rows correspond to observations, columns to variables. A `data.frame`, when `f` is not missing (s. below). An object of class `ExpressionSet`.
`y`	Class labels. Can be one of the following: A `numeric` vector. A `factor`. A `character` if `X` is an `ExpressionSet` that specifies the phenotype variable. `missing`, if `X` is a `data.frame` and a proper formula `f` is provided. WARNING: The class labels will be re-coded to range from `0` to `K-1`, where `K` is the total number of different classes in the learning set.
`f`	A two-sided formula, if `X` is a `data.frame`. The left part correspond to class labels, the right to variables.
`learnind`	An index vector specifying the observations that belong to the learning set. May be `missing`; in that case, the learning set consists of all observations and predictions are made on the learning set.
`models`	a logical value indicating whether the model object shall be returned
`...`	Further arguments to be passed to `qda` from the package `MASS`

An object of class cloutput.

Excessive variable selection has usually to performed before qdaCMA can be applied in the p > n setting. Not reducing the number of variables can result in an error message.

Martin Slawski ms@cs.uni-sb.de

Anne-Laure Boulesteix boulesteix@ibe.med.uni-muenchen.de

McLachlan, G.J. (1992).

Discriminant Analysis and Statistical Pattern Recognition.

Wiley, New York

compBoostCMA, dldaCMA, ElasticNetCMA, fdaCMA, flexdaCMA, gbmCMA, knnCMA, ldaCMA, LassoCMA, nnetCMA, pknnCMA, plrCMA, pls_ldaCMA, pls_lrCMA, pls_rfCMA, pnnCMA, rfCMA, scdaCMA, shrinkldaCMA, svmCMA

### load Golub AML/ALL data
data(golub)
### extract class labels
golubY <- golub[,1]
### extract gene expression from first 3 genes
golubX <- as.matrix(golub[,2:4])
### select learningset
ratio <- 2/3
set.seed(112)
learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
### run QDA
qdaresult <- qdaCMA(X=golubX, y=golubY, learnind=learnind)
### show results
show(qdaresult)
ftable(qdaresult)
plot(qdaresult)
### multiclass example:
### load Khan data
data(khan)
### extract class labels
khanY <- khan[,1]
### extract gene expression from first 4 genes
khanX <- as.matrix(khan[,2:5])
### select learningset
set.seed(111)
learnind <- sample(length(khanY), size=floor(ratio*length(khanY)))
### run QDA
qdaresult <- qdaCMA(X=khanX, y=khanY, learnind=learnind)
### show results
show(qdaresult)
ftable(qdaresult)
plot(qdaresult)