Real Datasets Application"
In MultiGroupO: MultiGroup Method and Simulation Data Analysis

knitr::opts_chunk$set(
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[vignetteMult](vignetteMult.html "MultiGroupO vignette")
[datR](datR.html "Real Datasets Application")

Description

Gene expression data from Khan et al. (2001). This data set contains 83 samples with 2308 genes: 29 cases of Ewing sarcoma (EWS), coded 1, 11 cases of Burkitt lymphoma (BL), coded 2, 18 cases of neuroblastoma (NB), coded 3, 25 cases of rhabdomyosarcoma (RMS), coded 4. A total of 63 training samples and 25 test samples are provided in Khan et al. (2001). Five of the test set are non-SRBCT and are not considered here. The training sample indexes correspond to 1:65 and the test sample indexes (without non-SRBCT sample) correspond to 66:83.

Standard PCA method

library(plsgenomics)
library(MultiGroupO)
data(SRBCT)
 mydata<-SRBCT$X
 mydata<-mydata[,1:5]
 groups<-as.factor(SRBCT$Y)
 pca(datos=mydata,grupos=groups,Plot=TRUE,center=TRUE,scale=TRUE)

Multigroup PCA method

library(plsgenomics)
data(SRBCT)
mydata<-SRBCT$X
mydata<-mydata[,1:5]
groups<-as.factor(SRBCT$Y)
mat.to.diag1<-new.cov(x=mydata,cls=groups,A=diag(ncol(mydata)))
mgpca(mat.to.diag=mat.to.diag1,mat.x=as.matrix(mydata),cls=groups,Plot=TRUE,ncomp=2,center = TRUE,scale = TRUE)

MDR method

```r library(plsgenomics) data(SRBCT) mydata<-SRBCT$X mydata<-mydata[,1:5] groups<-as.factor(SRBCT$Y) mydata<-split(as.data.frame(mydata),groups) mdr(group=groups,data.x=mydata,c=2)