pamr.batchadjust {pamr}R Documentation

A function to mean-adjust microarray data by batches

Description

A function to mean-adjust microarray data by batches

Usage

pamr.batchadjust(data)

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.

Details

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

Value

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

Author(s)

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

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)


[Package pamr version 1.57 Index]