Biobase

A Simple Aggregation Mechanism.

Biobase Package Overview

Utility classes for length one (scalar) objects

Retrieve Meta-data from eSets and ExpressionSets.

Add Menu Items to an Existing/New Menu of Window

Methods for Function annotatedDataFrameFrom in Package ‘Biobase’

Checks if there are any missing values in an object or not

Retrieve assay data from eSets and ExpressionSets.

Evaluate an expression if its value is not already cached.

Create a new ExpressionSet instance by selecting a specific channel

Retrieve and set channel names from object

Class Containing Measured Variables and Their Meta-Data Description.

Class "AssayData"

Class to Contain and Describe High-Throughput Expression Level Assays.

Class for Storing Microarray Experiment Information

MIAxE objects

Class to Contain and Describe High-Throughput Expression Level Assays.

Class to contain data from multiple channel array technologies

Class to Contain Objects Describing High-Throughput SNP Assays.

Class "Versioned"

Class "VersionedBiobase"

Class "Versions"

Class "VersionsNull"

A Simple Class for Aggregators

Class to Make Older Versions Compatible

A Lockable List Structure with Constraints on Content

Class to Contain High-Throughput Assays and Experimental Metadata

Retrieve information about versioned classes

Function to retrieve contents of environments

List-Environment interactions

Copy Between Connections or Files with Configure-Like Name-Value Substitution

Create a Package Directory from a Template

Dataset: Names and Characteristics of Amino Acids

Sample expression matrix and phenotype data.frames.

Example data.frame representing reporter information

Dataset of class 'ExpressionSet'

Data set of class 'MultiSet'

Biobase Deprecated and Defunct

Retrieve and set overall experimental information eSet-like classes.

Dump Textual Description of a Package

An apply-like function for ExpressionSet and related structures.

Retrieve expression data from eSets.

Retrieve information on features recorded in eSet-derived classes.

Retrieve feature and sample names from eSets.

List Vignette Files for a Package

Internals

Use version information to test whether class is current

Determine Unique Elements

Determine whether object or class contains versioning information

Compute the longest common prefix or suffix of a string

Lengths of list elements

Make an R package from a data object

Nearest neighbor search.

Assign Values to a Names

Informational Messages

Retrieve and set eSet notes.

Open PDF Files in a Standard Viewer

Open a Vignette or Show Vignette Selection Menu

Report Version of a Package

Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.

Protocol Metadata

Read and write 'AnnotatedDataFrame'

Read MIAME Information into an Instance of Class 'MIAME'

Read 'ExpressionSet'

A function to reverse the role of names and values in a list.

Calculates the median for each row in a matrix

A function to compute empirical row quantiles.

Create a new NChannelSet instance by selecting specific channels

Extract elements of a vector for concise rendering

Get and retrieve SNP call and call probability data.

Retrieve or set storage mode for eSets.

Break Character Strings to Fit Width

Extract the same element from the sublists of a list

A function to check internet connectivity to Bioconductor

Update an object to the class definition of a template

Update previously created eSet object to current eSet structure

A function to query the user for input

Conditionally append result to validity message