A function to mean-adjust microarray data by batches
A function to mean-adjust microarray data by batches
pamr.batchadjust(data)
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.
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
A data object of the same form as the input data, with x replaced by the adjusted x
Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.