Abstract
BackgroundMicroarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results.FindingsWe present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs.ConclusionCoupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.
Highlights
Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language
Microarray Я US was developed to provide a simple and streamlined workflow to researchers who are mainly interested in a fast differential gene expression analysis, and to improve the accuracy and reliability of the analysis, as well as expedite downstream functional analysis of the microarray results
In addition to many carefully planned design characteristics aimed at enhancing its usability, Microarray Я US provides the following unique features: Support custom chip description files (CDF) for major 3’IVT affymetrix GeneChips and probe re-annotation for major affymetrix GeneChips and illumina BeadArrays To enable researchers to take advantage of the latest research on probe set re-definition and re-annotation, we implemented the custom CDF and probe set reannotation by Dai et al (2005) and by Risueno et al (2010) for Affymetrix GeneChips and probe reannotation by Du et al (2008) and Barbosa-Morais et al (2009) for Illumina BeadArrays
Summary
A GUI to over a dozen widely used Bioconductor packages with enhanced usability, Microarray Я US provides a streamlined workflow for routine differential gene expression analysis based on Affymetrix and Illumina chips for users with no knowledge in R language. With its unique implementation of several up-to-date Affymetrix custom CDF and probe set re-annotations for both Affymetrix and Illumina platforms, this tool facilitates a more accurate and precise microarray data analysis. The versatile results output utility tool enables a fast and easy generation of input files for over 20 of the most popular functional analysis software programs. Additional file 1: List of the implemented Bioconductor packages. Complete list of the implemented Bioconductor packages with brief descriptions and references. Additional file 2: List of the supported functional analysis software. Description: Complete list of the supported functional analysis software for the Gene List Output Utility Tool. Additional file 3: List of the supported microarray data types. Complete list of the supported microarray chips. All authors participated in manuscript revisions and have read and approved the final manuscript
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