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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. |