R: A function to mean-adjust microarray data by batches

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.

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

    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 1.55 Index]