Normalization slides, HTML, PDF, Rmd

Quantile normalization example, PDF

Exercises

• 01_lowess_curve_fit_demo.R - Non-linear curve fitting exercise. code

• 02_lowess_by_hand_demo.R - Manually fitting Loess curves. code

• 03_lowess_2color.R - Loess on two-color arrays. MA diagnostic plots, global and print-tip loess normalization. code, data

• 04_normalization_affy.R - one-color array normalization, from scaling to loess. code, data

• 05_quantile_demo.R - quantile normalization of one-color array. code, data

References

On non-linear curve fitting and goodness-of-fit: “Technical note: Curve fitting with the R Environment for Statistical Computing”, PDF, http://www.css.cornell.edu/faculty/dgr2/teach/R/R_CurveFit.pdf

Misc

• qsmooth R package - Smooth quantile normalization (qsmooth) is a generalization of quantile normalization, which is an average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups. https://github.com/stephaniehicks/qsmooth