[BioC] how to cite "lumi"?

[Pan Du]

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) ²lumi: a pipeline for processing
Illumina microarray², Bioconductor package version 1.5.18.


For the VST (variance stabilization transformation) algorithm, please cite:
Lin, S.M., Du, P., Kibbe, W.A., ²Model-based Variance-stabilizing
Transformation for Illumina Microarray Data², Nucleic Acids Res. 2008 Jan 4

For nuID annotation packages, please cite:
Du, P., Kibbe, W.A. and Lin, S.M., ²nuID: A universal naming schema of
oligonucleotides for Illumina, Affymetrix, and other microarrays², 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