Quality metrics on microarray data sets


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Documentation for package ‘arrayQualityMetrics’ version 2.4.3

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addXYfromGAL Computing the coordinates of the spots on a slide
addXYfromGAL-methods Computing the coordinates of the spots on a slide
aqm.boxplot Performs boxplots on aqmobj.prepdata objects.
aqm.density Performs density plots on aqmobj.prepdata objects.
aqm.heatmap Performs dendrogram on aqmobj.prepdata objects.
aqm.maplot Performs MA-plots on aqmobj.prepdata objects.
aqm.meansd Performs Mean/SD plot on aqmobj.prepdata objects.
aqm.nuse Performs NUSE plot on aqmobj.prepaffy objects.
aqm.pca Performs Principal Component Analysis on aqmobj.prepdata objects.
aqm.plot Performs plots from aqm objects.
aqm.plot,aqmobj.box-method Performs plots from aqm objects.
aqm.plot,aqmobj.dens-method Performs plots from aqm objects.
aqm.plot,aqmobj.msd-method Performs plots from aqm objects.
aqm.plot,aqmobj.nuse-method Performs plots from aqm objects.
aqm.plot,aqmobj.pmmm-method Performs plots from aqm objects.
aqm.plot,aqmobj.qcs-method Performs plots from aqm objects.
aqm.plot,aqmobj.rle-method Performs plots from aqm objects.
aqm.plot,aqmobj.rnadeg-method Performs plots from aqm objects.
aqm.plot,aqmTrellis-method Performs plots from aqm objects.
aqm.plot-methods Performs plots from aqm objects.
aqm.pmmm Performs perfect match versus mismatch density plots.
aqm.prepaffy Preparation of Affymetrix experiments for RLE and NUSE.
aqm.prepdata Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.prepdata,AffyBatch-method Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.prepdata,aqmOneCol-method Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.prepdata,BeadLevelList-method Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.prepdata,ExpressionSet-method Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.prepdata,NChannelSet-method Generate an object aqmobj.prepdata to be called by the aqm functions.
aqm.probesmap Performs probes mapping on aqmobj.prepdata objects.
aqm.qcstats Performs QCstats plot on AffyBatch.
aqm.rle Performs RLE plot on aqmobj.prepaffy objects.
aqm.rnadeg Performs RNA degradation plot on AffyBatch.
aqm.spatial Performs spatial distribution representation of the arrays from aqmobj.prepdata objects.
aqm.spatialbg Performs spatial distribution representation of background intensities of the arrays from aqmobj.prepdata objects.
aqm.writereport Writes a report from objects produced with aqm.xxx functions.
aqmobj.box Class to contain data generated from aqm.boxplot.
aqmobj.box-class Class to contain data generated from aqm.boxplot.
aqmobj.dens Class to contain data generated from aqm.density.
aqmobj.dens-class Class to contain data generated from aqm.density.
aqmobj.heat Class to contain data generated from aqm.heatmap.
aqmobj.heat-class Class to contain data generated from aqm.heatmap.
aqmobj.ma Class to contain data generated from aqm.maplot.
aqmobj.ma-class Class to contain data generated from aqm.maplot.
aqmobj.msd Class to contain data generated from aqm.meansd.
aqmobj.msd-class Class to contain data generated from aqm.meansd.
aqmobj.nuse Class to contain data generated from aqm.nuse.
aqmobj.nuse-class Class to contain data generated from aqm.nuse.
aqmobj.pca Class to contain data generated from aqm.pca.
aqmobj.pca-class Class to contain data generated from aqm.pca.
aqmobj.pmmm Class to contain data generated from aqm.pmmm.
aqmobj.pmmm-class Class to contain data generated from aqm.pmmm.
aqmobj.prepaffy Class to contain data generated from aqm.prepaffy.
aqmobj.prepaffy-class Class to contain data generated from aqm.prepaffy.
aqmobj.prepdata Class to contain data generated from aqm.prepdata.
aqmobj.prepdata-class Class to contain data generated from aqm.prepdata.
aqmobj.probesmap Class to contain data generated from aqm.probesmap.
aqmobj.probesmap-class Class to contain data generated from aqm.probesmap.
aqmobj.qcs Class to contain data generated from aqm.qcs.
aqmobj.qcs-class Class to contain data generated from aqm.qcs.
aqmobj.rle Class to contain data generated from aqm.rle.
aqmobj.rle-class Class to contain data generated from aqm.rle.
aqmobj.rnadeg Class to contain data generated from aqm.rnadegplot.
aqmobj.rnadeg-class Class to contain data generated from aqm.rnadegplot.
aqmobj.spatial Class to contain data generated from aqm.spatial.
aqmobj.spatial-class Class to contain data generated from aqm.spatial.
aqmobj.spatialbg Class to contain data generated from aqm.spatialbg.
aqmobj.spatialbg-class Class to contain data generated from aqm.spatialbg.
arrayQualityMetrics Quality metrics on microarray experiments
arrayQualityMetrics,AffyBatch-method Quality metrics on microarray experiments
arrayQualityMetrics,aqmInputObj-method Quality metrics on microarray experiments
arrayQualityMetrics,BeadLevelList-method Quality metrics on microarray experiments
arrayQualityMetrics,ExpressionSet-method Quality metrics on microarray experiments
arrayQualityMetrics,MAList-method Quality metrics on microarray experiments
arrayQualityMetrics,marrayNorm-method Quality metrics on microarray experiments
arrayQualityMetrics,marrayRaw-method Quality metrics on microarray experiments
arrayQualityMetrics,NChannelSet-method Quality metrics on microarray experiments
arrayQualityMetrics,RGList-method Quality metrics on microarray experiments
arrayQualityMetrics-methods Quality metrics on microarray experiments
class.aqmobj.box Class to contain data generated from aqm.boxplot.
class.aqmobj.dens Class to contain data generated from aqm.density.
class.aqmobj.heat Class to contain data generated from aqm.heatmap.
class.aqmobj.ma Class to contain data generated from aqm.maplot.
class.aqmobj.msd Class to contain data generated from aqm.meansd.
class.aqmobj.nuse Class to contain data generated from aqm.nuse.
class.aqmobj.pca Class to contain data generated from aqm.pca.
class.aqmobj.pmmm Class to contain data generated from aqm.pmmm.
class.aqmobj.prepaffy Class to contain data generated from aqm.prepaffy.
class.aqmobj.prepdata Class to contain data generated from aqm.prepdata.
class.aqmobj.probesmap Class to contain data generated from aqm.probesmap.
class.aqmobj.qcs Class to contain data generated from aqm.qcs.
class.aqmobj.rle Class to contain data generated from aqm.rle.
class.aqmobj.rnadeg Class to contain data generated from aqm.rnadegplot.
class.aqmobj.spatial Class to contain data generated from aqm.spatial.
class.aqmobj.spatialbg Class to contain data generated from aqm.spatialbg.