Week 7

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This journal entry is due on Thursday, October 17, at 12:01am Pacific time.

Objectives

The purpose of this assignment is:

• to conduct the "analyze" step of the data life cycle for a DNA microarray dataset.
• to develop an intuition about what different p-value cut-offs mean.
• to keep a detailed electronic laboratory notebook to facilitate reproducible research.
• to revisit the "Deception at Duke" case with new insights because you have analyzed your own dataset.

Individual Journal Assignment

• Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).
• Invoke your template on your journal entry page so that you:
  • Link from your journal entry page to this Assignment page.
  • Link from your journal entry to your user page.
  • Add the "Journal Entry" category to the end of your wiki page.
• Because you have invoked your template on your user page, you should also have a:
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
• Include both the Acknowledgments and References section as specified by the Week 1 assignment.
• For your assignment this week, the electronic laboratory notebook you will keep on your individual wiki page is crucial. 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.
  • We will be performing a series of computations on a microarray dataset, primarily using Microsoft Excel. In the interests of reproducible research, it is appropriate to copy and paste the methods from this assignment into your individual journal entry.
  • You must then modify the general instructions (which are generic to the whole class) to your own data analysis, recording the specific modifications and equations that you used on your dataset.
  • Record the answers to the questions posed in the protocol at the place in which they appear in the method. You do not need to separate them out in a different results section.
  • All files generated in the protocol must be uploaded to the wiki and linked to from your journal entry page in a "Data and Files" section.
  • You will write a summary paragraph that gives the conclusions from this week's analysis.

Homework Partners

You will work in groups of two for this week's assignment. Please sit next to your partner in class. You will be expected to consult with your partner, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

• Aby and Iliana
• Christina and Mike
• David and DeLisa
• Emma and Joey
• Ivy and Kaitlyn
• Jonar and Marcus
• Mihir and Naomi

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 7 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).