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