yaqc.affy {yaqcaffy}R Documentation

Generate QC stats from an AffyBatch object

Description

Generate YAQC metrics for Affymetrix data.

Usage

yaqc.affy(object,tgt=100,tau=0.015,logged=FALSE)

Arguments

object a object of type AffyBatch or ExpressionSet
tgt the target intensity to which the chips should be scaled (used to calculated the GCOS intensities)
tau used by detection p value
logged to be used with an ExpressionSet object, defining if the expression intensities are logged

Details

Affymetrix recommend 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 and ExpressionSet object. In the first case, it computess GCOS intensity values, MAS 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)

[Package yaqcaffy version 1.2.0 Index]