Exploratory Analysis of Biological Data 2016

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Class Photo

Class photo

Recorded Lectures’ Playlist

Setup Instructions

Let’s begin - start here by installing the first “project” we will work with, as soon as you come in:

Place a pink PostIt on your laptop screen so we know you are working on these instructions.
Make sure you have a “workshop directory” (perhaps called “training”) in which you install all the RStudio “projects” we will be working with.
You must have R installed. If you don’t, install R now.
You must have RStudio installed. If you don’t, install RStudio now.
open RStudio
Select File → NewProject…
Click on Version Control
Click on Git
Enter https://github.com/hyginn/R_EDA-Introduction as the Repository URL.
Click on Browse… to find your training directory…
(The project-directory name should autofill to R_EDA-Introduction)
Click Create Project; the project files should be downloaded and the console should prompt you to type init() to begin.
Type init() into the console pane.
Place a green PostIt if this has worked for you; place a pink PostIt if you run into issues or have questions.

YouTube Playlist for Recorded Lectures

Day 1

Welcome

Ann Meyer

Module 1: Exploratory Data Analysis

Boris Steipe

Link to R Project repo: Enter https://github.com/hyginn/R_EDA-Introduction as the Repository URL.

**Before we move on: let’s list our progress! **

Helpful Links:

Module 2: Regression Analysis

Boris Steipe

Link to R Project repo: Enter https://github.com/hyginn/R_EDA-Regression as the Repository URL.

In RStudio, make a new project from https://github.com/hyginn/R_EDA-Regression as the Repository URL

**Before we move on: let’s list our progress! **

Links:

Maximal Information Coefficient
Homepage for data exploration with the MIC measure
CRAN: package MINERVA (R wrapper for a fast mine implementation)

Module 3: Dimension Reduction

Boris Steipe

Link to R Project repo: Enter https://github.com/hyginn/R_EDA-DimensionReduction as the Repository URL.

In RStudio, make a new project from https://github.com/hyginn/R_EDA-DimensionReduction as the Repository URL

**Before we move on: let’s list our progress! **

Integrated Assignment Part 1

Lauren Erdman and Ben Brew

Day 2

Module 4: Clustering Analysis

Boris Steipe

Scripts:

Link to R Project repo: Enter https://github.com/hyginn/R_EDA-Clustering as the Repository URL.

Comparison of Clustering Methods
R-“task view”: Cluster Analysis (and Finite Mixture Models)

Dataset:

If you load using Gset.RData do:

  load("gset.RData")

on the command line. (Check that ‘gset’ is actually lower case in the folder. You might need a capital letter at the start.)

If you load using Platf.RData do:

  load("platf.RData")

R object file: GSE26922.rds

Read with:

  gset <- readRDS("GSE26922.rds")
  # do not run the following line:
  gset <- gset [ [ idx ] ]

Module 5: Hypothesis Testing for EDA

Boris Steipe

Scripts:

Link to R Project repo: Enter https://github.com/hyginn/R_EDA-HypothesisTesting as the Repository URL.