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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 | Compute boxplots, density plots, heatmap, PCA biplot on a aqmobj.prepdata object. |
| aqm.density | Compute boxplots, density plots, heatmap, PCA biplot on a aqmobj.prepdata object. |
| aqm.heatmap | Compute boxplots, density plots, heatmap, PCA biplot on a aqmobj.prepdata object. |
| aqm.maplot | Performs MA-plots on aqmobj.prepdata objects. |
| aqm.meansd | Performs Mean/SD plot on aqmobj.prepdata objects. |
| aqm.nuse | Performs RLE and NUSE plots on aqmobj.prepaffy objects. |
| aqm.pca | Compute boxplots, density plots, heatmap, PCA biplot on a aqmobj.prepdata object. |
| aqm.plot | Performs plots from aqm objects. |
| aqm.plot-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-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 and NUSE plots on aqmobj.prepaffy objects. |
| aqm.rnadeg | Computes 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 the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.box-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.dens | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.dens-class | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.heat | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.heat-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.ma | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.ma-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| 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 the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.nuse-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.pca | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.pca-class | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| 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.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.probesmap-class | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.qcs | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.qcs-class | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.rle | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.rle-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| 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 the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.spatial-class | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| aqmobj.spatialbg | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| aqmobj.spatialbg-class | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| arrayQualityMetrics | Quality metrics for microarray experiments |
| arrayQualityMetrics-method | Quality metrics for microarray experiments |
| arrayQualityMetrics-methods | Quality metrics for microarray experiments |
| class.aqmobj.box | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.dens | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| class.aqmobj.heat | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.ma | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.msd | Class to contain data generated from aqm.meansd. |
| class.aqmobj.nuse | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.pca | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| 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.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| class.aqmobj.qcs | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| class.aqmobj.rle | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.rnadeg | Class to contain data generated from aqm.rnadegplot. |
| class.aqmobj.spatial | Class to contain data generated from the aqm.boxplot, aqm.heatmap, aqm.maplot, aqm.spatial, aqm.nuse and aqm.rle functions. |
| class.aqmobj.spatialbg | Class to contain data generated from aqm.density, aqm.pca, aqm.spatialbg, aqm.probesmap, aqm.qcs. |
| ksOutliers | Function for outlier determing potential outliers |