normalizing: Normalization of the dataMatrix

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

Normalization of the dataMatrix

Description

Normalization of the dataMatrix intensities

Usage

normalizing(
  x,
  method.vc = "pqn",
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiAssayExperiment'
normalizing(
  x,
  method.vc = "pqn",
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'SummarizedExperiment'
normalizing(
  x,
  method.vc = "pqn",
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiDataSet'
normalizing(
  x,
  method.vc = "pqn",
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'ExpressionSet'
normalizing(
  x,
  method.vc = "pqn",
  report.c = c("none", "interactive", "myfile.txt")[2]
)

Arguments

x	An S4 object of class SummarizedExperiment or MultiAssayExperiment
method.vc	character of length 1 or the total number of datasets: method(s) to be used for each dataset (default is 'pqn'); in case the parameter is of length 1 and x contains multiple datasets, the same method will be used for all datasets
report.c	character(1): File name with '.txt' extension for the printed results (call to sink()'); if 'interactive' (default), messages will be printed on the screen; if 'none', no verbose will be generated

Value

SummarizedExperiment or MultiAssayExperiment including the (list of) matrix with normalized intensities

Examples

sacurine.se <- reading(file.path(system.file(package = "phenomis"),
                                 "extdata/W4M00001_Sacurine-statistics"))
sacurine.se <- sacurine.se[, colnames(sacurine.se) != 'HU_neg_096_b2']
sacurine.se <- transforming(sacurine.se, method.vc = "log10")
norm.se <- normalizing(sacurine.se, method.vc = "pqn")
# MultiDataSet

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.