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 limma/limmaGUI 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 and Speed TP (2003). “Normalization of cDNA microarray data.” Methods, 31, pp. 265-273. If you use limma/limmaGUI for pre-processing or normalization of two-color microarray data, please cite this article which describes the functions read.maimages, normalizeWithinArrays, normalizeBetween-Arrays etc, including the use of spot quality weights.

Smyth GK, Michaud J and Scott H (2005). “The use of within-array replicate spots for assessing differential expression in microarray experiments.” Bioinformatics, 21, pp. 2067-2075. If you use the duplicateCorrection function to handle duplicate spots or technical replication, please cite this article.

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.

Smyth GK and Wettenhall JM (2004). “limmaGUI: a graphical user interface for linear modeling of microarray data.” Bioinformatics, 20, pp. 3705-3706. The limmaGUI software itself should be cited using this article.