A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

Lars M T Eijssen, Varshna S Goelela, Thomas Kelder, Michiel E Adriaens, Chris T Evelo, Marijana Radonjic

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

BACKGROUND: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. RESULTS: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. CONCLUSIONS: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.
Original languageEnglish
Article number482
JournalBMC Genomics
Volume16
DOIs
Publication statusPublished - 1 Jan 2015

Keywords

  • Computational Biology
  • Internet
  • Oligonucleotide Array Sequence Analysis
  • Quality Control
  • User-Computer Interface

Cite this

@article{74f9ab8a6488497195cb5e1cab503e1b,
title = "A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal",
abstract = "BACKGROUND: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. RESULTS: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. CONCLUSIONS: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.",
keywords = "Computational Biology, Internet, Oligonucleotide Array Sequence Analysis, Quality Control, User-Computer Interface",
author = "Eijssen, {Lars M T} and Goelela, {Varshna S} and Thomas Kelder and Adriaens, {Michiel E} and Evelo, {Chris T} and Marijana Radonjic",
year = "2015",
month = "1",
day = "1",
doi = "10.1186/s12864-015-1689-8",
language = "English",
volume = "16",
journal = "BMC Genomics",
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A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal. / Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana.

In: BMC Genomics, Vol. 16, 482, 01.01.2015.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

AU - Eijssen, Lars M T

AU - Goelela, Varshna S

AU - Kelder, Thomas

AU - Adriaens, Michiel E

AU - Evelo, Chris T

AU - Radonjic, Marijana

PY - 2015/1/1

Y1 - 2015/1/1

N2 - BACKGROUND: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. RESULTS: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. CONCLUSIONS: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

AB - BACKGROUND: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. RESULTS: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. CONCLUSIONS: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

KW - Computational Biology

KW - Internet

KW - Oligonucleotide Array Sequence Analysis

KW - Quality Control

KW - User-Computer Interface

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VL - 16

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 482

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