SPH 247 Statistical Analysis of Laboratory Data
Spring 2015

Course Sylabus

Class 1, March 31, 2015:

Experimental Design
ANOVA
Assignment 1

Endocrin Data Set (CSV)
Endocrin Data Set Documentation
Endocrine input code

Fasting Glucose Data Set (tab delimited)
Fasting Glucose input code

Class 2, April 7, 2015

Regression and Calibration
Analytical Error
Assignment 2

Zinc data set

Class 3, April 14, 2015:

Assays--PCR, ELISA, Luminex
Gene Expression Arrays
Exercises
Assignment 1 Solutions

HIV Data Set
AD Data Set

Bob Rice's Affymetrix Data

LN0A.CEL, LN0B.CEL, LN1A.CEL, LN1B.CEL, LN2A.CEL, LN2B.CEL
LN3A.CEL, LN3B.CEL, LN4A.CEL, LN4B.CEL, LN5A.CEL, LN5B.CEL

Class 4, April 21, 2015:

Introduction to Assays
Basic Array Analysis
Assignment 2 Solutions

Class 5, April 28, 2015:

DNA Sequencing
Next Gen Sequencing
RNA-Seq
RNA-Seq Review Paper
Assignment 3 Solutions

Class 6, May 5, 2015:

RNA-Seq Analysis with limma
GO and Annotation
Bottomly Count Data
Bottomly Pheno Data
Bottomly input code
Bottomly limma analysis code
Assignment 4

Class 7, May 12, 2015:

Annotation with R
AnnotationDbi in R
Annotation with DAVID
DAVID Tutorial
Nature Protocols Paper
Assignment 5

Class 8, May 19, 2015:

Generalized Linear Models/Classification
Measures of Classification Success
Prediction and Classification
Personalized Medicine
Assignment 6

Class 9, May 26, 2015

Multivariate Analysis
Clustering
Assignment 7
Assignment 6 Solutions