# Quality metrics report for microarray data sets

## Documentation for package ‘arrayQualityMetrics’ version 3.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addXYfromGAL | Computing the coordinates of the spots on a slide
addXYfromGAL-methods | Computing the coordinates of the spots on a slide
aqm.boxplot | Functions for computing quality report modules.
aqm.density | Functions for computing quality report modules.
aqm.heatmap | Functions for computing quality report modules.
aqm.maplot | Functions for computing quality report modules.
aqm.meansd | Functions for computing quality report modules.
aqm.nuse | Functions for computing quality report modules.
aqm.pca | Functions for computing quality report modules.
aqm.pmmm | Functions for computing quality report modules.
aqm.probesmap | Functions for computing quality report modules.
aqm.rle | Functions for computing quality report modules.
aqm.rnadeg | Functions for computing quality report modules.
aqm.spatial | Functions for computing quality report modules.
aqm.writereport | Write a quality report
aqmReportModule | Class to contain all the information to render a quality report module.
aqmReportModule-class | Class to contain all the information to render a quality report module.
arrayQualityMetrics | Quality metrics for microarray experiments
boxplotOutliers | Helper functions for outlier detection and reporting in arrayQualityMetrics
class:aqmReportModule | Class to contain all the information to render a quality report module.
class:outlierDetection | Represents the results from applying an outlier detection criterion to the arrays.
outlierDetection | Represents the results from applying an outlier detection criterion to the arrays.
outlierDetection-class | Represents the results from applying an outlier detection criterion to the arrays.
outliers | Helper functions for outlier detection and reporting in arrayQualityMetrics
prepaffy | Compute useful summary statistics from a data object.
prepdata | Compute useful summary statistics from a data object.