NMPP: a user-customized NimbleGen microarray data processing pipeline

NMPP: a user-customized NimbleGen microarray data processing pipeline

UNLABELLED 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, t...

ArrayPipe: a flexible processing pipeline for microarray data

A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range fr...

lumi: a pipeline for processing Illumina microarray

UNLABELLED Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix ...

A Flexible Pipeline for Experimental Design, Processing, and Analysis of Microarray Data

We created a web-based microarray data analysis pipeline for managing the volumes of data created by production microarray experiments. Experiments are formalized by grouping array data into hierarchies based on types such as 'dye swap' or 'replicate.' Grouping determines the analysis to be performed and enables the tool to automatically generate reports and charts appropriate to the experiment...

cDNA Microarray Data Normalization