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

In pamr: Pam: Prediction Analysis for Microarrays

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.

This object if the same form as that produced by pamr.from.excel.

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

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)

Example output

Loading required package: cluster
Loading required package: survival

pamr documentation built on May 2, 2019, 12:35 p.m.