Windows InstallationMac OS InstallationLinux Installation
Implemented MethodsKey Bioconductor PackagesCustom CDF and Probe ReannotationSupported Functional Analysis Software
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University of Southern California

Microarray Я US  

Reliable statistical and comprehensive functional analysis of microarray data made easy—Harness the power of Bioconductor tools without learning R language!
Last Updated: Mar 19, 2013 URL: http://norris.usc.libguides.com/MicroarrayRUS Print Guide RSS Updates

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What is "Microarray Я US"?

Featuring a user-friendly graphic interface, Microarray Я US is an R-based program that seamlessly integrates functions from over a dozen or so most-widely used Bioconductor packages to offer researchers a streamlined workflow to perform routine microarray expression data analysis without the need of learning R language. 

 

Key Features

  • An intuitive graphic user interface
    enables users to use many popular Bioconductor microarray data analysis tools with little or no knowledge of Bioconductor/R language.
  • Complete data analysis workflow
    covers data import, quality control, pre-processing, differential expression analysis, and power analysis.
  • Supports major chips from Affymetrix and Illumina
    enables quick analysis of both user-provided data and public data from GEO/ArrayExpress.
  • Latest custom chip description files (CDF) and probe re-annotation 
    allows more accurate analysis and interpretation of both Affymetrix and Illumina data. For more on implemented custom CDF and probe re-annotation, check out this page.
  • Provides algorithms lacking in some commercial software
    Implements some widely used algorithms for pre-processing (such as MAS5 and dChip) and differential expression analysis (such as Limma, SA, maSigPro).
  • Versatile gene list output utility tool
    allows automatic and easy generation of input files for over 20 most widely used functional analysis software, including Ingenuity Pathway Analysis, NextBio, DAVID, GSEA, GeneTrail, WebGestalt, GeneCodis, GenMAPP, Onto-tools, GoMiner, MAGIA, The Connectivity Map, GenePattern, etc. For more information on these software, check out this page.
  • Multiple OS compatibility
    supports Microsoft Windows, Mac OS and Linux operating systems.
 

Microarray Я US Workflow

 

Supported Platforms

Affymetrix GeneChip (.CEL file):  

  • Human: HG-U133A; HG-U133A_2; HG-U133B; HG-U133_Plus_2; HG_U95A; HG_U95Av2; HG_Focus
  • Mouse: MG_U74Av2; MG_U74Bv2; MG_U74Cv2; Mouse430_2; Mouse430A_2; MOE430A; MOE430B
  • Rat: RG_U34A; Rat230_2; RAE230A; RAE230B

Illumina BeadArray (output from BeadStudio or GenomeStudio):

  • Human (versions 1 to 3): HumanWG-6; HumanRef-8; HumanHT-12
  • Mouse (versions 1 to 2):  MouseWG-6; MouseRef-8
  • Rat (version 1): RatRef-12

 

What's New

Microarray Я US v.1.0 is released.

Please fill out the registration form to get access to the program. 

Any comments, suggestions, bug reports are welcomed! 

     

    How to cite this work?

    Please cite the following paper:

    Microarray R US: a user-friendly graphical interface to bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    BMC Res Notes. 2012 Jun 8;5(1):282.

    Yilin Dai1*, Ling Guo1*, Meng Li2, and Yi-Bu Chen2*

    1. Department of Mathematical Sciences, Michigan Technological University;

    2. Bioinformatics Service Program, Norris Medical Library, University of Southern California


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