basicPLM: Simplified interface to PLM.

In oligo: Preprocessing tools for oligonucleotide arrays

Description

Simplified interface to PLM.

Usage

basicPLM(pmMat, pnVec, normalize = TRUE, background = TRUE, transfo =
  log2, method = c('plm', 'plmr', 'plmrr', 'plmrc'), verbose = TRUE)

Arguments

pmMat	Matrix of intensities to be processed.
pnVec	Probeset names
normalize	Logical flag: normalize?
background	Logical flag: background adjustment?
transfo	function: function to be used for data transformation prior to summarization.
method	Name of the method to be used for normalization. 'plm' is the usual PLM model; 'plmr' is the (row and column) robust version of PLM; 'plmrr' is the row-robust version of PLM; 'plmrc' is the column-robust version of PLM.
verbose	Logical flag: verbose.

Value

A list with the following components:

Estimates	A (length(pnVec) x ncol(pmMat)) matrix with probeset summaries.
StdErrors	A (length(pnVec) x ncol(pmMat)) matrix with standard errors of 'Estimates'.
Residuals	A (nrow(pmMat) x ncol(pmMat)) matrix of residuals.

Note

Currently, only RMA-bg-correction and quantile normalization are allowed.

Author(s)

Benilton Carvalho

See Also

rcModelPLM, rcModelPLMr, rcModelPLMrr, rcModelPLMrc, basicRMA

Examples

set.seed(1)
pms <- 2^matrix(rnorm(1000), nc=20)
colnames(pms) <- paste("sample", 1:20, sep="")
pns <- rep(letters[1:10], each=5)
res <- basicPLM(pms, pns, TRUE, TRUE)
res[['Estimates']][1:4, 1:3]
res[['StdErrors']][1:4, 1:3]
res[['Residuals']][1:20, 1:3]

oligo documentation built on Nov. 8, 2020, 6:52 p.m.