Affymetrix QC

How to cite ArrayAnalysis.org? 

User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.
Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Müller M, Evelo CT.
Nucleic Acids Res. 2013 Apr 24. PMID: 23620278
doi: dx.doi.org/10.1093/nar/gkt293

Abstract | Full Text | PDF

For the statistical and pathway analysis module please also cite 

Adding automated Statistical Analysis and Biological Evaluation modules to www.arrayanalysis.org
Master's thesis of Anwesha Bohler (Dutta)
Advisor : Lars M.T. Eijssen
doi: dx.doi.org/10.13140/2.1.5150.6244

Google Scholar | ResearchGate

For the Illumina analysis

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Lars M.T. Eijssen1, Varshna S. Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo and Marijana Radonjic
doi: dx.doi.org/10.1186/s12864-015-1689-8

Full Text