Multiple testing correction slides, HTML, PDF, Rmd

Batch effect correction slides HTML, PDF, Rmd

Exercises

• Multiple testing correction demo, multitest.R

• Permutation p-value, permutations.R

• Example of batch effect correction using ComBat and SVA http://jtleek.com/genstats/inst/doc/02_13_batch-effects.html, batch_sva_combat.R

References

• Original q-value paper

Storey, John D., and Robert Tibshirani. “Statistical Significance for Genomewide Studies.” PNAS 2003 http://www.pnas.org/content/100/16/9440.long

• A two-page overview of multiple testing correction

Krzywinski, Martin, and Naomi Altman. “Points of Significance: Comparing Samples—part II.” Nature Methods 2014 http://www.nature.com/nmeth/journal/v11/n4/full/nmeth.2900.html

• An overview of the batch effect problem

Leek, Jeffrey T., et. al., and Rafael A. Irizarry. “Tackling the Widespread and Critical Impact of Batch Effects in High-Throughput Data.” Nature Reviews. 2010 http://www.nature.com/nrg/journal/v11/n10/abs/nrg2825.html

• Original ComBat paper

Johnson, W. Evan, Cheng Li, and Ariel Rabinovic. “Adjusting Batch Effects in Microarray Expression Data Using Empirical Bayes Methods.” Biostatistics 2007 http://biostatistics.oxfordjournals.org/content/8/1/118.long

• SVA paper

Leek, Jeffrey T., and John D. Storey. “Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis.” PLoS Genetics 2007 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030161