oligo (version 1.36.1)

basicPLM: Simplified interface to PLM.

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.

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]