Statistical Methods for Bioinformatics

Winter 2014

January 8, 2014

## 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 2/3/13## pvadjust.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 Classification## Chicken.Proteomics.xlsx

Chicken.Factors.txt

Rice et al. 2012## Spuriousprediction.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 Analysis## Lymphoma 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 analysis## Brooks et al.

DESeq Package

DESeq Genome Biology

edgeR Bioinformatics

Cuffdiff2 Nature Biotechnology

## Assignment 5 Solutions

Assignment 6 Due 3/24/14

Cuffdiff2