Difference between revisions of "Week 8"
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* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>). | * Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>). | ||
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so). | * 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 [http://www.cbsnews.com/video/watch/?id=7398476n "Deception at Duke"]. | ||
| + | * View the video: [http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/ The Importance of Reproducible Research in High-Throughput Biology: Case Studies in Forensic Bioinformatics]. | ||
| + | * Review the slides from DataONE on [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx data entry and manipulation]. | ||
| + | * Optional: for more information on the Duke saga, see the web site put together by Baggerly and Coombes [http://bioinformatics.mdanderson.org/Supplements/ReproRsch-All/Modified/StarterSet/ 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 [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) paper]. Do you think there is sufficient information there for '''''you''''' to reproduce their data analysis? Why or why not? | ||
[[Category:Assignment]] | [[Category:Assignment]] | ||
Revision as of 06:17, 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:
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.
- For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
Homework Partners
For this week, the homework partners will be:
- 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?
