BASH - Compact Defect Analysis
Boxplots from summary data
Storage of annotation information
View beadarray User's Guide
Add probe data
backgroundCorrectSingleSection
Background correct an array-section
BASH - Diffuse Defect Analysis
The beadarray package: a tool for low-level analysis of Illumina BeadArrays
BASH - Extended Defect Analysis
BASH - BeadArray Subversion of Harshlight
Outlier distribution stats
Calculate detection scores
Convert a BeadLevelList object into a beadLevelData object
A function to generate a targets file given a directory of Illumina bead-level files
Tabulate QC scores
Combine two objects.
Percentage of beads detected
Deprecated Functions
Retrieve the dimensions of an object
beadRegistrationData-class
Class "beadRegistrationData"
Get raw data from a beadLevelData object
ExpressionSetIllumina-class
Class "ExpressionSetIllumina"
HULK - Bead Array Normalization by NEighbourhood Residuals
Retrieve control beads
Differential expression using limma
Gets the number of beads from a beadLevelData object
Plot outlier locations
Read ``.locs'' file.
Read the Illumina tiff images
returns all beads with weight=0.
Annotation definitions
Function to construct the classic MA plots from a dataset
Plotting the intensities of selected beads on a section
Read BeadScan gene expression output
Read bead-level Illumina data
Perform check for misregistered array segments.
Class "BeadLevelList"
Create files for a Gene Expression Omnibus submission
GEO required fields
Show Array Mask
Accessing metrics information in bead-level objects
Median normalise data in a matrix
Classify each bead according to its control status
Identifier outliers on an array section
Plot the positive controls
Prepare iScan data for use with beadarray
Set weights from BASH
Display object summary
Class "limmaResults"
Class "illuminaChannel"
Plot bead locations
Image processing functions
imageplot for beadLevelData object
Function to Plot the Layout of an Illumina BeadChip
Scatter plots and MA-plots for all specified arrays
Produce plots of the Illumina tiff images
Flexible bead-level QC pipeline
Add, modify or remove data in a beadLevelData object
Generate matrix of neighbouring beads
Modify the sectionData slot
returns no outliers on an array section
Create summary values for specified IDs
Normalise Illumina expression data
Read BeadStudio gene expression output
Read a Sample sheet for a BeadArray experiment
Gets the section names from a beadLevelData Object
Create a summarized object
Identifier outliers on an array section
Functions for transforming the data store in a beadLevelData object for easier visualisation or summarisation.