DepthTools: an R package for a robust analysis of gene expression data

BMC Bioinformatics

Aurora Torrente²  Sara López-Pintado³  Juan Romo¹ 

[1] Departamento de Estadística, Universidad Carlos III de Madrid, C/ Madrid, 126, 28903, Getafe, Spain

[2] Departamento de Ciencia e Ingeniería de Materiales e Ingeniería Química, Universidad Carlos III de Madrid, Av Universidad, 30, 28911, Leganés, Spain

[3] Departamento de Economía, Métodos Cuantitativos e Historia Económica, Universidad Pablo de Olavide, Carretera de Utrera, Km 1, 41013, Sevilla, Spain

关键词: R commander plug-in;    R package;    Robustness;    Data depth;   

Others  :  1087799
DOI  :  10.1186/1471-2105-14-237

 received in 2013-04-24, accepted in 2013-07-17,  发布年份 2013

【 摘 要 】

Background

The use of DNA microarrays and oligonucleotide chips of high density in modern biomedical research provides complex, high dimensional data which have been proven to convey crucial information about gene expression levels and to play an important role in disease diagnosis. Therefore, there is a need for developing new, robust statistical techniques to analyze these data.

Results

depthTools is an R package for a robust statistical analysis of gene expression data, based on an efficient implementation of a feasible notion of depth, the Modified Band Depth. This software includes several visualization and inference tools successfully applied to high dimensional gene expression data. A user-friendly interface is also provided via an R-commander plugin.

Conclusion

We illustrate the utility of the depthTools package, that could be used, for instance, to achieve a better understanding of genome-level variation between tumors and to facilitate the development of personalized treatments.

【 授权许可】

   
2013 Torrente et al.; licensee BioMed Central Ltd.

【 图 表 】

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