yaqc.affy: 'YAQCStats' constructor

In yaqcaffy: Affymetrix expression data quality control and reproducibility analysis

Description

Generate YAQC metrics for Affymetrix data.

Usage

 yaqc.affy(object,
myYaqcControlProbes=NULL,
alphas=NULL,
tgt=100,
tau=0.015,
logged,
verbose) 

Arguments

object	a object of type AffyBatch or ExpressionSet.
myYaqcControlProbes	an object of type YaqcControlProbes. If none is supplied (default behaviour), the control probes are selected automatically. See the YaqcControlProbes class for more details probeSelectionInterface to generate such an object.
alphas	a numeric of length 2 with the alpha1 and alpha2 values. Alpha1 and alpha2 are thresholds used to define if a given probe shoudl be called present (p<alpha1), marginal (alpha1<p<alpha2) or absent (alpha2<p), where p is the p-value from the Wilcoxon Signed Rank test used in MAS5. The default is to get these values from simpleaffy's qcdef files (see simpleaffy's vignette for more details) or to use 0.04 and 0.06 as default values.
tgt	the target intensity to which the chips should be scaled (used to calculated the MAS5 intensitiy values).
tau	used for detection p-value.
logged	to be used with an ExpressionSet object, defining if the expression intensities are logged.
verbose	logical value. If 'TRUE', it writes out some messages indicating progress. If 'FALSE' nothing should be printed.

Details

Affymetrix recommends a set of quality control metrics to check the quality of GeneChips expression arrays. This function applies the guidelines described in the Affymetrix Microarray Quality Control Consortium (MAQC) protocols to asses the succes of the hybridization. See the package vignette for more details.

This function takes a raw (unnormalised) AffyBatch object or an ExpressionSet object. In the first case, it computes MAS5 intensity values, expression calls(see call.exprs) and other quality-related metrics to generate an YAQCStats. If an ExpressionSet object is provided, only the β-actin, GAPDH and internal control values are computed.

Value

An YAQCStats object describing the input object

Author(s)

Laurent Gatto

Examples

    ## loading data
    library(affydata)
    data(Dilution)
    ## qc analysis
    qobj <- yaqc(Dilution)
    show(qobj)

yaqcaffy documentation built on Nov. 8, 2020, 8:31 p.m.