nomadNormalization: Apply anova model to mass spec data. Use residuals of anova...

In carlmurie/NOMAD: Normalization of Mass Spectrometry Data

Description

Apply anova model to mass spec data. Use residuals of anova model as final scores.

Usage

nomadNormalization(y, x, factors = NULL, doRobust = TRUE, doLog = TRUE,
  doiTRAQCorrection = FALSE, iTRAQCorrectionTable = NULL)

Arguments

y	real Dependant variable (vector of positive real numbers)
x	matrix Independent or explanatory variables (matrix). In this context they will be "Peptide","Protein", "Run", and "iTRAQ" identifiers. An optional "iTRAQCorrectionIndex" column is necessary if iTRAQ isotope correction is desired.
factors	vector Default is to use the 4 main factors (Peptide, Protein, Run, and iTRAQ) and the three interactions between Run and the other three main effects. The user can define their own factors. The "factors" list must match the data.frame labels of x.
doRobust	logical If TRUE use medians of levels instead of the default means. Default is to use median.
doLog	logical If TRUE then y will be logged (log 2). Default is to log.
doiTRAQCorrection	logical If true then orrect peptide abundance scores based on their iTRAQ labelling. Default is TRUE. iTRAQ correction values are hardcoded for 8 iTRAQs. The iTRAQCorrectionTable must be provided for iTRAQs that do not number 8.
iTRAQCorrectionTable	matrix Matrix of iTRAQ corrections. If iTRAQ equals 8 then an internal correction table is used. If a table is provided when iTRAQ equals 8 then the user supplied table will be used. If the number of iTRAQs is not eight than a table must be supplied by the user.

Value

List elements are y: normalized scores after anova normalization, x: design matrix, removedData: index of rows removed from input data, call: function call.

Examples

data(BalfPeptides)

ret <- nomadNormalization(y=BalfPeptides$Abundance, x=BalfPeptides)

carlmurie/NOMAD documentation built on May 14, 2019, 11:12 a.m.