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

BMC Research Notes

Yi-Bu Chen²  Meng Li²  Ling Guo¹  Yilin Dai¹ 

[1] Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49934, USA;Bioinformatics Service Program, Norris Medical Library, University of Southern California, 2003 Zonal Ave, Los Angeles, CA, 91007, USA

关键词: Probe reannotation;    Gene expression;    Microarray data analysis;   

Others  :  1166335
DOI  :  10.1186/1756-0500-5-282

 received in 2012-02-06, accepted in 2012-04-18,  发布年份 2012

【 摘 要 】

Background

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. 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.

Findings

We 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.

Conclusion

Coupled 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.

【 授权许可】

   
2012 Dai et al.; licensee BioMed Central Ltd.

【 图 表 】

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