pamr.batchadjust

0th

Percentile

A function to mean-adjust microarray data by batches

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) 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

Aliases
  • pamr.batchadjust
Examples
# NOT RUN {
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)
# }
Documentation reproduced from package pamr, version 1.56.1, License: GPL-2

Community examples

Looks like there are no examples yet.