Affymetrix QC

How to cite 

User-friendly solutions for microarray quality control and pre-processing on
Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Müller M, Evelo CT.
Nucleic Acids Res. 2013 Apr 24. PMID: 23620278

Abstract | Full Text | PDF

For the statistical and pathway analysis module please also cite 

Adding automated Statistical Analysis and Biological Evaluation modules to
Master's thesis of Anwesha Bohler (Dutta)
Advisor : Lars M.T. Eijssen

Google Scholar | ResearchGate

For the Illumina analysis

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the portal
Lars M.T. Eijssen1, Varshna S. Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo and Marijana Radonjic

Full Text