Introduction to Assays
Regression, Calibration, and Analytical Error
zinc.csv
Currie (1995)
Rocke and Lorenzato (1995)
Wilson, Rocke, Durbin, and Kahn (2004)
Supplementary Lecture: R Basics
Data Transformations
Assays Part 1
Assignment 1 Due in Class 1/27/14
hiv.csv
AD-Luminex.csv
Data Manipulation in R for the zinc data
Mass Spectrometry
Gene Expression Arrays
Gene Expression Arrays
Analysis of Gene Expression Data
Assignment 2 Due in Class 2/3/13pvadjust.R
LN0A.CEL, LN0B.CEL, LN1A.CEL, LN1B.CEL, LN2A.CEL, LN2B.CEL
LN3A.CEL, LN3B.CEL, LN4A.CEL, LN4B.CEL, LN5A.CEL, LN5B.CEL
Assignment 1 Solutions
Annotation and the Gene Ontology
Annotation with R
Annotation with DAVID
Variance Estimation and Normalization of Arrays
Assignment 3 Due in Class 2/10/14
Nature Protocols DAVID.pdf
Generalized Linear Models
Assignment 2 Solutions
Proteomics Analysis
Prediction and ClassificationChicken.Proteomics.xlsx
Chicken.Factors.txt
Rice et al. 2012Spuriousprediction.r
Spuriousprediction3.r
Spuriousprediction3.r
Spuriousprediction4.r
Assignment 3 Solutions
Proteomics Part 2
Prediction Quality and the ROC Curve
No Class—Presidents' Day
Assignment 4 Due in Class 2/26/14
Multivariate AnalysisLymphoma Data
array.data.zip
array.data.csv
ArrayID.txt
Alizadeh et al. (2000)
Prediction and Classification
Friedman et al 2008
Tibshirani et al 2010
Clustering
Assignment 5 Due in Class 3/12/14
Personalized Medicine
DNA Sequencing (from Dan Russell—Power Point, but only looks right on a Mac)
Illumina Sequencing (pdf from Illumina 2010)
NGS and RNA-Seq
Assignment 4 Solutions
DESeq
pasilla data set and analysisBrooks et al.
DESeq Package
DESeq Genome Biology
edgeR Bioinformatics
Cuffdiff2 Nature Biotechnology
Assignment 5 Solutions
Assignment 6 Due 3/24/14
Cuffdiff2