References

  • A Moussa, B Vannier, M Maouene. (2012). "New Algorithm for Gene Selection in Microarray Data Analysis Workflow." Computer Technology and Application 3(2): 169-174.

  • Liu, W. M., et al. (2002). "Analysis of high density expression microarrays with signed-rank call algorithms." Bioinformatics 18(12): 1593-1599.

  • Zhu, Q., et al. (2010). "Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset." BMC Bioinformatics 11: 285.

  • Bolstad, B. M., et al. (2003). "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias." Bioinformatics 19(2): 185-193.

  • Tusher, V. G., et al. (2001). "Significance analysis of microarrays applied to the ionizing radiation response." Proc Natl Acad Sci U S A 98(9): 5116-5121.

Package references

  • Shiny: Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2015). shiny: Web Application Framework for R. R package version 0.11.1. http://CRAN.R-project.org/package=shiny

  • affy: Gautier, L., Cope, L., Bolstad, B. M., and Irizarry, R. A. 2004. affy---analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 3 (Feb. 2004), 307-315.

  • affyPLM: Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Dissertation. University of California, Berkeley.

  • limma: Smyth, GK (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397-420.

  • siggenes: Holger Schwender (2012). siggenes: Multiple testing using SAM and Efron's empirical Bayes approaches. R package version 1.38.0.

  • twilight: Stefanie Scheid (). twilight: Estimation of local false discovery rate. R package version 1.40.0. http://compdiag.molgen.mpg.de/software/twilight.shtml

  • genefilter: R. Gentleman, V. Carey, W. Huber and F. Hahne (). genefilter: genefilter: methods for filtering genes from microarray experiments. R package version 1.46.1.

  • VennDiagram: Hanbo Chen (2014). VennDiagram: Generate high-resolution Venn and Euler plots. R package version 1.6.9. http://CRAN.R-project.org/package=VennDiagram