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