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