A modular storage and analysis pipeline for quality control, analysis and MAGE-ML export of microarray data

General info

Date from - to

13 Jun 2005

Project leader(s)

Prof. dr. F.C.P. Holstege

Theme

Microarray technology

Abstract

A rate-limiting step in applying microarrays is data handling. This includes extraction of raw signal intensities, quality control, experiment annotation, up to date array annotation, storage of other relevant information, analysis at several levels and in multiple ways, visualization, publication and exchange of data. Standards for microarray data are under development but only a few groups have experience in implementing these standards. Dissemination and implementation of microarray data standards at the national level is one important goal of this project. As part of this dissemination, the project foresees in developing a pipeline for all aspects of microarray handling, which is comprehensive, flexible, efficient and include incorporation of microarray data standards for publication and exchange. The modular nature allows separate parts to be implemented elsewhere as well as incorporation of contributions from other projects. The pipeline will serve a wide body of microarray users and will also be a training platform for microarray data analysis.

Version 1.1 of the pipeline has been implemented, and is used and tested by the UMC Utrecht microarray facility. This includes batch upload and annotation of experiments. We continue to write R scripts for further statistical exploration of results.