Experimental design slides, HTML, Rmd

QC spotted (two-channel) arrays slides, HTML, PDF, Rmd

QC Affymetrix (single-channel) arrays slides, HTML, PDF, Rmd

Exercises

• MAplots_QC_spotted.R - Reading in two spotted arrays, playing with regular and Bland-Altman plots. code, data

• MAplots_affy.R - constructing ExpressionSet, visualizing it as scatterplot, MAplot, smoothscatter. Volcano plot. code, data

• Affy_QC.R - reading CEL files, plotting probes, boxplots, affyPLM visualization, average background, percent present, 3’/5’ ratio. code, data

• LOF_code.R - lack of fit test using Affymetrix spike-in data, code

References

• Quality Assessment of Exon and Gene 1.0 ST Arrays (pdf, 180 KB) http://www.affymetrix.com/support/technical/whitepapers/exon_gene_arrays_qa_whitepaper.pdf

• Manufacturing Quality Control and Validation Studies of GeneChip® Arrays (pdf, 3.28 MB) http://www.affymetrix.com/support/technical/technotes/manufacturing_quality_technote.pdf

Misc

• mimager: The microarray imager R package https://github.com/aaronwolen/mimager