Kzebrows Week 15

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.