readQC {beadarray}R Documentation

Read and plot Illumina quality control information

Description

Reads the standard format of Illumina quality control information and produces diagnostic plots

Usage

readQC(file, columns=list(Biotin="AVG.Signal.biotin", cy3_high="AVG.Signal.cy3_hyb_high", cy3_low="AVG.Signal.cy3_hyb_low", cy3_med="AVG.Signal.cy3_hyb_med", gene="AVG.Signal.gene", hs="AVG.Signal.high_stringency_hyb", house="AVG.Signal.housekeeping", labeling="AVG.Signal.labeling", mm="AVG.Signal.low_stringency_hyb_mm2", pm="AVG.Signal.low_stringency_hyb_pm", negative="AVG.Signal.negative"),skip=7,sep=",",header=T)
plotQC(object,...)

Arguments

file name of file containing qc information
columns a vector of column names to read from the file
skip number of lines of header information to ignore in the file
header if TRUE the column names in the file are read
sep a character string for the file separator
object a ExpressionSetIllumina object containing QC information or QC object created by readQC
... extra plotting arguments that can be sent to plotQC

Details

The default options are able to read a file which gives quality control information and put in a sensible data structure. The quality control files are generated by BeadStudio and given the file name _qc_info.csv by default.

The information read is given in a assayData structure with Signal (average expression), Var (standard error) and Detection matrices. The rows of each matrix are arrays in the experiment and columns are the average value of a particular control type.

A plot giving a overview of all the control types can be produced by using plotQC. We can also plot a particular control using singleQCPlot and specify whether to plot the average, standard deviation or detection.

Value

readQC produces an assayData object with Signal, Var and Detection matrices

Author(s)

Mark Dunning

Examples


data(QC)

QC$Signal

data(BSData)

QC = QCInfo(BSData)



[Package beadarray version 1.2.2 Index]