Entry: addXYfromGAL
Aliases: addXYfromGAL-methods addXYfromGAL
Keywords: file manip
Description: Computing the coordinates of the spots on a slide
URL: ../../../library/arrayQualityMetrics/html/XYfromGAL.html

Entry: aqm.boxplot
Aliases: aqm.boxplot
Keywords: 
Description: Performs boxplots on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.boxplot.html

Entry: aqm.density
Aliases: aqm.density
Keywords: 
Description: Performs density plots on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.density.html

Entry: aqm.heatmap
Aliases: aqm.heatmap
Keywords: 
Description: Performs dendrogram on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.heatmap.html

Entry: aqm.maplot
Aliases: aqm.maplot
Keywords: 
Description: Performs MA-plots on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.maplot.html

Entry: aqm.meansd
Aliases: aqm.meansd
Keywords: 
Description: Performs Mean/SD plot on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.meansd.html

Entry: aqm.nuse
Aliases: aqm.nuse
Keywords: 
Description: Performs NUSE plot on aqmobj.prepaffy objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.nuse.html

Entry: aqm.pca
Aliases: aqm.pca
Keywords: 
Description: Performs Principal Component Analysis on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.pca.html

Entry: aqm.plot
Aliases: aqm.plot aqm.plot-methods aqm.plot,aqmTrellis-method aqm.plot,aqmobj.box-method aqm.plot,aqmobj.dens-method aqm.plot,aqmobj.msd-method aqm.plot,aqmobj.nuse-method aqm.plot,aqmobj.pmmm-method aqm.plot,aqmobj.qcs-method aqm.plot,aqmobj.rle-method aqm.plot,aqmobj.rnadeg-method
Keywords: 
Description: Performs plots from aqm objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.plot.html

Entry: aqm.pmmm
Aliases: aqm.pmmm
Keywords: 
Description: Performs perfect match versus mismatch density plots.
URL: ../../../library/arrayQualityMetrics/html/aqm.pmmm.html

Entry: aqm.prepaffy
Aliases: aqm.prepaffy
Keywords: 
Description: Preparation of Affymetrix experiments for RLE and NUSE.
URL: ../../../library/arrayQualityMetrics/html/aqm.prepaffy.html

Entry: aqm.prepdata
Aliases: aqm.prepdata aqm.prepdata,ExpressionSet-method aqm.prepdata,AffyBatch-method aqm.prepdata,NChannelSet-method aqm.prepdata,BeadLevelList-method aqm.prepdata,aqmOneCol-method
Keywords: 
Description: Generate an object aqmobj.prepdata to be called by the aqm functions.
URL: ../../../library/arrayQualityMetrics/html/aqm.prepdata.html

Entry: aqm.probesmap
Aliases: aqm.probesmap
Keywords: 
Description: Performs probes mapping on aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.probesmap.html

Entry: aqm.qcstats
Aliases: aqm.qcstats
Keywords: 
Description: Performs QCstats plot on AffyBatch.
URL: ../../../library/arrayQualityMetrics/html/aqm.qcstats.html

Entry: aqm.rle
Aliases: aqm.rle
Keywords: 
Description: Performs RLE plot on aqmobj.prepaffy objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.rle.html

Entry: aqm.rnadeg
Aliases: aqm.rnadeg
Keywords: 
Description: Performs RNA degradation plot on AffyBatch.
URL: ../../../library/arrayQualityMetrics/html/aqm.rnadeg.html

Entry: aqm.spatial
Aliases: aqm.spatial
Keywords: 
Description: Performs spatial distribution representation of the arrays from aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.spatial.html

Entry: aqm.spatialbg
Aliases: aqm.spatialbg
Keywords: 
Description: Performs spatial distribution representation of background intensities of the arrays from aqmobj.prepdata objects.
URL: ../../../library/arrayQualityMetrics/html/aqm.spatialbg.html

Entry: aqm.writereport
Aliases: aqm.writereport
Keywords: 
Description: Writes a report from objects produced with aqm.xxx functions.
URL: ../../../library/arrayQualityMetrics/html/aqm.writereport.html

Entry: aqmobj.box-class
Aliases: aqmobj.box-class aqmobj.box class.aqmobj.box
Keywords: classes
Description: Class to contain data generated from aqm.boxplot.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.box.html

Entry: aqmobj.dens-class
Aliases: aqmobj.dens-class aqmobj.dens class.aqmobj.dens
Keywords: classes
Description: Class to contain data generated from aqm.density.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.dens.html

Entry: aqmobj.heat-class
Aliases: aqmobj.heat-class aqmobj.heat class.aqmobj.heat
Keywords: classes
Description: Class to contain data generated from aqm.heatmap.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.heat.html

Entry: aqmobj.ma-class
Aliases: aqmobj.ma-class aqmobj.ma class.aqmobj.ma
Keywords: classes
Description: Class to contain data generated from aqm.maplot.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.ma.html

Entry: aqmobj.msd-class
Aliases: aqmobj.msd-class aqmobj.msd class.aqmobj.msd
Keywords: classes
Description: Class to contain data generated from aqm.meansd.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.msd.html

Entry: aqmobj.nuse-class
Aliases: aqmobj.nuse-class aqmobj.nuse class.aqmobj.nuse
Keywords: classes
Description: Class to contain data generated from aqm.nuse.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.nuse.html

Entry: aqmobj.pca-class
Aliases: aqmobj.pca-class aqmobj.pca class.aqmobj.pca
Keywords: classes
Description: Class to contain data generated from aqm.pca.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.pca.html

Entry: aqmobj.pmmm-class
Aliases: aqmobj.pmmm-class aqmobj.pmmm class.aqmobj.pmmm
Keywords: classes
Description: Class to contain data generated from aqm.pmmm.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.pmmm.html

Entry: aqmobj.prepaffy-class
Aliases: aqmobj.prepaffy-class aqmobj.prepaffy class.aqmobj.prepaffy
Keywords: classes
Description: Class to contain data generated from aqm.prepaffy.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.prepaffy.html

Entry: aqmobj.prepdata-class
Aliases: aqmobj.prepdata-class aqmobj.prepdata class.aqmobj.prepdata
Keywords: classes
Description: Class to contain data generated from aqm.prepdata.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.prepdata.html

Entry: aqmobj.probesmap-class
Aliases: aqmobj.probesmap-class aqmobj.probesmap class.aqmobj.probesmap
Keywords: classes
Description: Class to contain data generated from aqm.probesmap.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.probesmap.html

Entry: aqmobj.qcs-class
Aliases: aqmobj.qcs-class aqmobj.qcs class.aqmobj.qcs
Keywords: classes
Description: Class to contain data generated from aqm.qcs.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.qcs.html

Entry: aqmobj.rle-class
Aliases: aqmobj.rle-class aqmobj.rle class.aqmobj.rle
Keywords: classes
Description: Class to contain data generated from aqm.rle.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.rle.html

Entry: aqmobj.rnadeg-class
Aliases: aqmobj.rnadeg-class aqmobj.rnadeg class.aqmobj.rnadeg
Keywords: classes
Description: Class to contain data generated from aqm.rnadegplot.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.rnadeg.html

Entry: aqmobj.spatial-class
Aliases: aqmobj.spatial-class aqmobj.spatial class.aqmobj.spatial
Keywords: classes
Description: Class to contain data generated from aqm.spatial.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.spatial.html

Entry: aqmobj.spatialbg-class
Aliases: aqmobj.spatialbg-class aqmobj.spatialbg class.aqmobj.spatialbg
Keywords: classes
Description: Class to contain data generated from aqm.spatialbg.
URL: ../../../library/arrayQualityMetrics/html/aqmobj.spatialbg.html

Entry: arrayQualityMetrics
Aliases: arrayQualityMetrics arrayQualityMetrics-methods arrayQualityMetrics,ExpressionSet-method arrayQualityMetrics,AffyBatch-method arrayQualityMetrics,NChannelSet-method arrayQualityMetrics,BeadLevelList-method arrayQualityMetrics,RGList-method arrayQualityMetrics,MAList-method arrayQualityMetrics,marrayRaw-method arrayQualityMetrics,marrayNorm-method arrayQualityMetrics,aqmInputObj-method
Keywords: hplot
Description: Quality metrics on microarray experiments
URL: ../../../library/arrayQualityMetrics/html/arrayQualityMetrics.html
