Ksherbina Week 8

Katrina Sherbina

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Assignment Description

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 15

Class Journal

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Individual Journal

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Other

Week 5: Database Wiki

Final Project

Team H(oo)KD Project Page

Journal Club Presentation

Project Individual Journal

Lab Journal: Statistical Analysis of Vibrio cholerae Microarray Data

• Download the file Merrell_Compiled_Raw_Data_Vibrio.xls from the Sample Microarray Analysis for Vibrio cholerae page.
  • Save the file with the following format for the filename: Merrell_Compiled_Raw_Data_Vibrio_<Initials>_<Date>.xls
• Open the file. Insert a new worksheet and name it "scaled_centered".
• Go back to the "compiled_raw_data" worksheet. Select All and Copy. Go to your new "scaled_centered" worksheet, click on the upper, left-hand cell (cell A1) and Paste.
• Insert two rows in between the top row of the column headers and the first row of data.
• In cell A2, type "Average" and in cell A3, type "StdDev".
• Compute the average log fold change for each chip, which corresponds to each column of the data. In cell B2, type the following equation:

=AVERAGE(B4:B5224)

and hit Enter.

• Alternately, to select the range within the parenthesis of the AVERAGE formula, click on the first cell of the range for which the computation will be performed, scroll to the bottom of the the worksheet, and Shift+click on the last cell of the range.
• Click and hold the lower right hand corner of the cell B2. Then, drag the cursor to the last column for which you would like to compute the average log fold change.

• Compute the standard deviation of the log fold change ratios for each chip, which corresponds to each column of the data. In cell B3, type the following equation:

=STDEV(B4:B5224)

and hit Enter.

• Click and hold the lower right hand corner of the cell B3. Then, drag the cursor to the last column for which you would like to compute the standard deviation of the log fold change ratios.

The resulting Excel file can be downloaded here. The text file to be used for GenMapp can be downloaded here.

Lab Journal: MAPPFinder Analysis of Vibrio cholerae Microarray Data

1. Installed GenMAPP Classic from this [page] onto my computer.
2. Downloaded the following data files: Vc-Std_External_20090622.gdb and Vc-Std_External_20101022.gdb.