Difference between revisions of "Week 8"
From LMU BioDB 2015
Kdahlquist (Talk | contribs) (→Overview: two purposes of assignment) |
Kdahlquist (Talk | contribs) (→Homework Partners: compare and contrast work, meet outside of class) |
||
| Line 30: | Line 30: | ||
=== Homework Partners === | === Homework Partners === | ||
| − | + | The homework partners for this week are listed below. Initially, you will compare your analysis with your partner to check your work. Then, you and your partner will carry out two slightly different analyses and contrast them with each other. It will be vital for you and your partner to have at least one face-to-face meeting outside of class to complete this assignment. | |
* Mary Alverson, Kristin Zebrowski | * Mary Alverson, Kristin Zebrowski | ||
Revision as of 06:39, 15 October 2015
This journal entry is due on Tuesday, October 27, at midnight PDT. (Monday night/Tuesday morning)
Contents
Overview
The purpose of this assignment is:
- To gain an in depth understanding of how DNA microarray data is analyzed by carrying out all of the steps yourself on a dataset for which the "answers" are known.
- To introduce you to the process we will use for the final projects in the course using a series of in-class and journal assignments where we will first analyze microarray data from Vibrio cholerae, and then learn how to create a GenMAPP-compatible Gene Database for this organism.
Individual Journal Assignment
- Store this journal entry as "username Week 8" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
- Keep an "electronic lab notebook", containing your methods, results, and interpretations of the Vibrio cholerae microarray analysis part 1 and part 2 in your "username Week 8" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.
- Your electronic notebook should contain enough information such that you or someone else could reproduce what you did given only the information on your page.
- It is acceptable to copy and paste the methods from the protocol page into your electronic lab notebook as long as you cite the source and change it to reflect what you actually did.
- That means that you will often need to change the tense of the instructions from imperative to past tense, for example.
- You need to change the instructions if you did it differently than what is stated or did a subset of what is stated there.
- It is acceptable to copy and paste the methods from the protocol page into your electronic lab notebook as long as you cite the source and change it to reflect what you actually did.
- You should use screenshots and hyperlinks as appropriate to illustrate your notebook.
- Be sure to answer any questions embedded in the protocol. You do not need to make a separate section for these. I.e., the methods and results can be mixed.
- Your electronic notebook should contain enough information such that you or someone else could reproduce what you did given only the information on your page.
- Upload the requested files from part 1 and part 2 to this wiki and link to them on your individual journal page.
- IMPORTANT upload your completed spreadsheet (both the .xls and .txt versions) from part 1 by the interim deadline of midnight, Tuesday, October 20 (Monday night/Tuesday morning) so that Dr. Dahlquist can check them before moving on to part 2 of the exercise. She will not be assigning grades at this point; you will have the chance to make corrections, if necessary, before completing part 2.
Homework Partners
The homework partners for this week are listed below. Initially, you will compare your analysis with your partner to check your work. Then, you and your partner will carry out two slightly different analyses and contrast them with each other. It will be vital for you and your partner to have at least one face-to-face meeting outside of class to complete this assignment.
- Mary Alverson, Kristin Zebrowski
- Nicole Anguiano, Emily Simso
- Brandon Klein, Veronica Pacheco
- Josh Kuroda, Ronald Legaspi
- Brandon Litvak, Anu Varshneya
- Lena Olufson, Kevin Wyllie
- Trixie Roque, Erich Yanoschik
- Mahrad Saeedi, Jake Woodlee
- Store your journal entry in the shared Class Journal Week 8 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
View
Now that you've done your own microarray data analysis, we will revisit the case "Deception at Duke".
- View the video: The Importance of Reproducible Research in High-Throughput Biology: Case Studies in Forensic Bioinformatics.
- Review the slides from DataONE on data entry and manipulation.
- Optional: for more information on the Duke saga, see the web site put together by Baggerly and Coombes here.
Reflection
- What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?
- What recommendations does Dr. Baggerly recommend for reproducible research? How do these correspond to what DataONE recommends?
- Do you have any further reaction to this case after viewing Dr. Baggerly's talk?
- Go back to the Merrell et al. (2002) paper. Do you think there is sufficient information there for you to reproduce their data analysis? Why or why not?
