BIOL368/F14:Week 13: Difference between revisions
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=== View === | |||
Now that you've done your own microarray 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]. | |||
* View 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? | |||
* Look at the methods and results described in 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 to reproduce their data analysis? Why or why not? | |||
Revision as of 16:06, 29 October 2014
This journal entry is due on Wednesday, November 26 at midnight PST (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.
NOTE that this assignment is UNDER CONSTRUCTION.
View
Now that you've done your own microarray 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.
- View 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?
- Look at the methods and results described in the Merrell et al. (2002) paper. Do you think there is sufficient information there to reproduce their data analysis? Why or why not?
