Mdoyle Week 8
From OpenWetWare
Individual Journal Assignment
This journal entry is due on Monday, October 25 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.
- 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).
- Create the following set of links.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Link to this assignment from your journal entry.
- Add the "BIOL367/F10" category to the end of your wiki page.
- Keep an "electronic lab notebook", containing your methods, results, and interpretations of this week's portion of the Analysis of Vibrio cholerae microarray data project 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.
- Upload your completed spreadsheet to your individual journal page.
Electronic Lab Notebook
- In class, we began working with the data in Excel. I saved the changes made during class, and uploaded the file onto my wiki.
Sanity Checks
- Click on the drop-down arrow on your "Pvalue" column. Select "Custom". In the window that appears, set a criterion that will filter your data so that the Pvalue has to be less than 0.05.
- How many genes have p value < 0.05?
- What about p < 0.01?
- What about p < 0.001?
- What about p < 0.0001?
- The "Avg_LogFC_all" tells us the size of the gene expression change and in which direction. Positive values are increases relative to the control; negative values are decreases relative to the control.
- Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change greater than zero. How many are there?
- Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change less than zero. How many are there?
- What about an average log fold change of > 0.25 or < -0.25?
- What criteria did Merrell et al. (2002) use to determine a significant gene expression change? How does it compare to our method?
- Merrell et al. (2002) report that genes with IDs: VC0028, VC0941, VC0869, VC0051, VC0647, VC0468, VC2350, and VCA0583 were all significantly changed in their data. Look these genes up in your spreadsheet? What are their fold changes and p values? Are they significantly changed in our analysis?
