Vpachec3 Week 14
From LMU BioDB 2015
Revision as of 23:26, 3 December 2015 by Vpachec3 (Talk | contribs) (working on electronic notebook)
Thursday,December 3
- Kevin and I looked at Dr.Dahlquist's feedback on our spreadsheet so far.
- Based on what was said we used the file Raw_compiled_data_KD20151124.xls to continue the process.This was because Dr. Dahlquist made the point that our chip has each gene spotted in quadruplicate. These are considered technical replicates and they should be averaged before doing any further analysis.
- Thus, we took the average of the 4 technical replicates with the average function on excel.We selected the gene for each replicate individually. The function looked like
=AVERAGE(C2,M2,W2,AG2)
We then clicked on the small black square at the bottom of the cell to have the function repeat and adjust for the remaining cells.
- Then you need to average the averages for biofilm and for tobramycin. (It doesn't make sense to average biofilm and tobramycin together since they are separate treatments).
- Because your reference sample is genomic DNA and not RNA, you need to then take the ratio of the averages for the biofilm and tobramycin samples to get the ratio of tobramycin to control (tobramycin over biofilm). Because the numbers are in log space, you will subtract the biofilm average from the tobramycin average to get this number.
- You will conduct a two-sample t test comparing the 5 biofilm samples to the 3 tobramycin samples using the TTEST function in Excel, not the equation we did for Vibrio. It will directly compute the p value.
- Then you can compute the Bonferroni and Benjamini and Hochberg corrected p values like you did in the Vibrio exercise.
