ExpressionView-package {ExpressionView} | R Documentation

## The ExpressionView package

### Description

A package designed to interactively explore biclusters identified in gene expression data.

### Introduction

Clustering genes according to their expression profiles is an important task in analyzing microarray data. ExpressionView allows the user to explore the biclusters together with the underlying data in an interactive environment. The applet requires a browser with Adobe Flash player 10 installed.

The ExpressionView package can treat gene expression data in the form of a Bioconductor `ExpressionSet`. It recognizes biclusters identified by the Iterative Signature Algorithm (ISA) implemented in the `ISA` package as well as the methods available in the `biclust` package.

### Worflow

The usual workflow consist of three steps:

Order

  To arrange the possibly overlapping biclusters in a visually appealing layout, the gene expression data has to be reordered in such a way that individual biclusters from contiguous rectangles. The optimal order is found by the `OrderEV` function.

Export

  In a second step, the biclusters and all the relevant biological information are combined and exported to an ExpressionView XML file. This is done by the `ExportEV` function.

Visualize

  The Flash applet is started by the `LaunchEV` command. Video tutorials describing the various features of the applet can be found on the ExpressionView website (http://www.unil.ch/cbg/ExpressionView).

A tutorial can be found in the accompanying vignette of the package.

### Biclustering with non-gene expression data

Both, the `ISA` and the biclustering methods implemented in the `biclust` package can treat any two-dimensional data, i.e., not necessarily originating from gene expression profiling. While the ExpressionView package is optimized for gene expression matrices, it is also possible to explore data stemming from other sources. For more information, see the description of the `ExportEV` function.

### Author(s)

Andreas Lüscher andreas.luescher@a3.epfl.ch

### See Also

`OrderEV`, `ExportEV` and `LaunchEV`

[Package ExpressionView version 1.40.0 Index]