Smyth GK (2004). “Linear models and empirical Bayes methods for assessing differential expression in microarray experiments.” Statistical Applications in Genetics and Molecular Biology, 3, pp. No.1 Article 3. If you use affylmGUI/limma for differential expression analysis, please cite this article which describes the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes, topTable etc.

Smyth GK (2005). “Limma: linear models for microarray data.” In Gentleman R, Carey V, Dudoit S, Irizarry R and Huber W (eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor, chapter 23, pp. 397-420. Springer, New York. To cite the limma software itself please refer to this article which describes the software package in the context of the Bioconductor project and surveys the range of experimental designs for which the package can be used, including spotspecific dye-effects. The pre-processing capabilities of the package are also described but more briefly, with examples of background correction, spot quality weights and filtering with control spots. This article is also the best current reference for the normexp background correction method.

Wu Z, Irizarry RA, Gentleman R, Murillo FM and Spencer F (2004). “A Model Based Background Adjustment for Oligonucleotide Expression Arrays.” Journal of the American Statistical Association, 99, pp. 909-917. To cite the gcrma background correction method (GCRMA) please refer to this article which describes gcrma background adjustment procedure.

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP (2003). “Exploration, normalization, and summaries of high density oligonucleotide array probe level data.” Biostatistics, 4(2), pp. 249-264. To cite the robust multiarray average background correction method (RMA) please refer to this article which describes this procedure.

Wettenhall JM, Simpson KM, Satterley K and Smyth GK (2006). “affylmGUI: a graphical user interface for linear modeling of single channel microarray data.” Bioinformatics, 22, pp. 897-899. The affylmGUI software itself should be cited using this article.