getAdj: Extract values adjusted for unwanted variation by RUVm
In ChuanJ/test: Analysing Illumina HumanMethylation BeadChip Data

Description Usage Arguments Details Value Author(s) See Also Examples

Extract values adjusted for unwanted variation by RUVm.

1	getAdj(Y, fit)

`Y`	A matrix of M-values.
`fit`	The list `list` object produced by `RUVfit`.

This function extracts values adjusted for unwanted variation by RUVm. These values are ONLY intendeded to be used for visualisation purposes. It is NOT recommended that they are used for any further analysis.

An matrix of M-values.

Jovana Maksimovic jovana.maksimovic@mcri.edu.au

MArrayLM

if(require(minfi) & require(minfiData) & require(limma)) {

# Get methylation data for a 2 group comparison
meth <- getMeth(MsetEx)
unmeth <- getUnmeth(MsetEx)
Mval <- log2((meth + 100)/(unmeth + 100))

group <- factor(pData(MsetEx)$Sample_Group, labels=c(0,1))
design <- model.matrix(~group)

# Perform initial analysis to empirically identify negative control features 
# when not known a priori
lFit <- lmFit(Mval,design)
lFit2 <- eBayes(lFit)
lTop <- topTable(lFit2,coef=2,num=Inf)

# The negative control features should *not* be associated with factor of interest
# but *should* be affected by unwanted variation 
ctl <- rownames(Mval) %in% rownames(lTop[lTop$adj.P.Val > 0.5,])

# Perform RUV adjustment and fit
fit <- RUVfit(Y=Mval, X=group, ctl=ctl)
fit2 <- RUVadj(Y=Mval, fit=fit)

# get adjusted values
Madj <- getAdj(Y=Mval,fit=fit)
}