Hi Cei, Thanks for using the lumi package. Since our package paper is still under review (it is slow!), you may cite the package paper as: Du, P., Kibbe, W.A. and Lin, S.M., (2008) ?lumi: a pipeline for processing Illumina microarray?, Bioconductor package version 1.5.18. For the VST (variance stabilization transformation) algorithm, please cite: Lin, S.M., Du, P., Kibbe, W.A., ?Model-based Variance-stabilizing Transformation for Illumina Microarray Data?, Nucleic Acids Res. 2008 Jan 4 For nuID annotation packages, please cite: Du, P., Kibbe, W.A. and Lin, S.M., ?nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays?, Biology Direct 2007, 2:16 (31May2007) We will further improve the lumi package, especially the annotation and quality control parts. Thanks! Have a nice day, Pan On 4/9/08 5:24 AM, "Cei Abreu-Goodger" <cei at="" sanger.ac.uk=""> wrote: > Hi Pan, > > I wasn't sure if I should email this to the "bioconductor" mailing list, > since for now I'm only concerned with the lumi package. I want to know > how I should reference it. You mention a reference for VST, nuID and a > comparison paper in the lumi vignette. Suppose I didn't use VST or nuID, > but just used lumiR with log2/quantile normalization. What would be your > preference for citing lumi as a "general" package for processing > Illumina data? > > Many thanks, > > Cei > --------------------------------------------------- Pan Du, PhD Research Assistant Professor Robert H. Lurie Comprehensive Cancer Center Northwestern University 676 ST Clair St., #1200 Chicago, IL 60611 Office (312)695-4781 dupan at northwestern.edu