pamr (version 1.57)

pamr.batchadjust: A function to mean-adjust microarray data by batches

Description

A function to mean-adjust microarray data by batches

Usage

pamr.batchadjust(data)

Value

A data object of the same form as the input data, with x replaced by the adjusted x

Arguments

data

The input data. A list with components: x- an expression genes in the rows, samples in the columns, and y- a vector of the class labels for each sample, and batchlabels- a vector of batch labels for each sample.

Author

Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu

Details

pamr.batchadjust does a genewise one-way ANOVA adjustment for expression values. Let \(x(i,j)\) be the expression for gene \(i\) in sample \(j\). Suppose sample \(j\) in in batch \(b\), and let \(B\) be the set of all samples in batch \(b\). Then pamr.batchadjust adjusts \(x(i,j)\) to \(x(i,j) - mean[x(i,j)]\) where the mean is taken over all samples \(j\) in \(B\).

Examples

suppressWarnings(RNGversion("3.5.0"))
set.seed(120)
#generate some data
x <- matrix(rnorm(1000*20),ncol=20)
y <- sample(c(1:4),size=20,replace=TRUE)
batchlabels <- sample(c(1:5),size=20,replace=TRUE)
mydata <- list(x=x,y=factor(y),batchlabels=factor(batchlabels))

mydata2 <- pamr.batchadjust(mydata)