A user-customized NimbleGen Microarray Data Processing Pipeline

NMPP package is a bundle of user-customized tools that helps the researchers to process self-designed NimbleGen microarray data, developed by PERL programming scripts and compiled to be independent executable programs running on Windows MS-DOS command line mode and any version of Linux system. NMPP is functionalized in an integrative processing manner that collects a large amount of raw expression data from multiple microarray experiments, visualize array surface probe signal distribution, performs single-array background correction and multi-array normalizations, summarize gene expression intensity from multiple probes and replicate data points, and finally estimates gene expression status by a remodeled negative control distribution. Collectively, NMPP tools package provides researchers with a practical, prompt and effective way of processing custom-designed NimbleGen microarray data.