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. |