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.
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.


RESULTS
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.


CONCLUSIONS
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.
Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49934, USA.
Yilin
Y
Dai
Ling
L
Guo
Meng
M
Li
Yi-Bu
YB
Chen
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D003196:Computer Graphics; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D051381:Rats; D015203:Reproducibility of Results; D014584:User-Computer Interface