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Bioinformatics Advance Access originally published online on October 12, 2006
Bioinformatics 2006 22(23):2955-2957; doi:10.1093/bioinformatics/btl525
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

NMPP: a user-customized NimbleGen microarray data processing pipeline

Xiangfeng Wang 1,2,{dagger}, Hang He 3,{dagger}, Lei Li 2, Runsheng Chen 3, Xing Wang Deng 1,2,* and Songgang Li 1,*

1 Center of Bioinformatics & Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University Beijing 100871, China
2 Department of Molecular, Cellular, and Developmental Biology, Yale University New Haven, CT 06520, USA
3 Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, China

*To whom correspondence should be addressed.

Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene expression intensity summarization module and the gene expression status inference module.

Availability: http://plantgenomics.biology.yale.edu/nmpp

Contact: Xiangfeng.Wang{at}Yale.edu

Supplementary information: The supplementary materials, figures, testing dataset, software instructions and a typical workflow of using NMPP package are accessible through the above homepage.

Received on August 31, 2006; accepted on October 5, 2006

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