Difference between revisions of "Kzebrows Week 15"
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| + | Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files. | ||
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| + | Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo. | ||
{{Template:Kzebrows}} [[Category: Journal Entry]] | {{Template:Kzebrows}} [[Category: Journal Entry]] | ||
Revision as of 20:09, 12 December 2015
Contents
Electronic Lab Notebook
Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
- Opened Criterion-GO.txt file in Excel
- Filtered Excel file:
- Number Changed by between 4 and 100
- Z score by greater than 2
- PermuteP by less than 0.05
- Adjusted P by less than 0.1
Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the OTS Files page under GenMAPP User Files.
Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo.
Assignments
Individual Journal Assignment Pages
- 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 14
- Week 15
Individual Journal Assignments
- Kzebrows Week 1
- Kzebrows Week 2
- Kzebrows Week 3
- Kzebrows Week 4
- Kzebrows Week 5
- Kzebrows Week 6
- Kzebrows Week 7
- Kzebrows Week 8
- Kzebrows Week 9
- Kzebrows Week 10
- Kzebrows Week 11
- Kzebrows Week 12
- Kzebrows Week 14
- Kzebrows Week 15
- Final Individual Reflection
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Oregon Trail Survivors Week 10
- Oregon Trail Survivors Week 11
- Oregon Trail Survivors Week 12
- Oregon Trail Survivors Week 14
Additional Links
- User Page: Kristin Zebrowski
- Class Page: BIOL/CMSI 367-01
- Team Page: Oregon Trail Survivors
