Difference between revisions of "Ksherbina Week 8"
From LMU BioDB 2013
(Added section to record steps to complete the MAPPFinder analysis. Italicized text in the first header.) |
(→Lab Journal: MAPPFinder Analysis of Vibrio cholerae Microarray Data: Added steps to download GenMAPP and the data files.) |
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==Lab Journal: MAPPFinder Analysis of ''Vibrio cholerae'' Microarray Data== | ==Lab Journal: MAPPFinder Analysis of ''Vibrio cholerae'' Microarray Data== | ||
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| + | #Installed GenMAPP Classic from this [[http://www.genmapp.org/download_v2.1.php page]] onto my computer. | ||
| + | #Downloaded the following data files: [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020090622/Vc-Std_External_20090622.zip/download Vc-Std_External_20090622.gdb] and [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download Vc-Std_External_20101022.gdb]. | ||
[[Category:Journal Entry]] | [[Category:Journal Entry]] | ||
[[Category:Individual Homework]] | [[Category:Individual Homework]] | ||
Revision as of 17:01, 15 October 2013
| 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.
- Rename the file in the following format: 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 headers and the first data row.
- In cell A2, type "Average" and in cell A3, type "StdDev".
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
- Installed GenMAPP Classic from this [page] onto my computer.
- Downloaded the following data files: Vc-Std_External_20090622.gdb and Vc-Std_External_20101022.gdb.
