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Exploratory Analysis of Biological Data 2016

Workshop pages for students



Course Schedule

Schedule for June 7 to June 8, 2016

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Class Photo

Class photo

Setup Instructions

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

  1. Place a pink PostIt on your laptop screen so we know you are working on these instructions.
  2. Make sure you have a “workshop directory” (perhaps called “training”) in which you install all the RStudio “projects” we will be working with.
  3. You must have R installed. If you don’t, install R now.
  4. You must have RStudio installed. If you don’t, install RStudio now.
  5. open RStudio
  6. Select File → NewProject…
  7. Click on Version Control
  8. Click on Git
  9. Enter https://github.com/hyginn/R_EDA-Introduction as the Repository URL.
  10. Click on Browse… to find your training directory…
  11. (The project-directory name should autofill to R_EDA-Introduction)
  12. Click Create Project; the project files should be downloaded and the console should prompt you to type init() to begin.
  13. Type init() into the console pane.
  14. 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

Recorded Lectures’ Playlist


Day 1

Welcome

Ann Meyer

Module 1: Exploratory Data Analysis

Boris Steipe

Lecture

Recorded Lecture

Recorded Lecture

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

Lecture

Recorded Lecture

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:


Module 3: Dimension Reduction

Boris Steipe

Lecture

Recorded Lecture

Recorded Lecture

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

Lecture

Assignment

Assignment Questions

Data Set

Plot.R


Day 2

Module 4: Clustering Analysis

Boris Steipe

Lecture

Recorded Lecture

Scripts:

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

  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

Lecture

Recorded Lecture

Scripts:

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


View on GitHub