Difference between revisions of "Ntesfaio Week 8"
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Does NSR1 change expression due to cold shock in this experiment? | Does NSR1 change expression due to cold shock in this experiment? | ||
| − | Only at higher time points | + | Only at higher time points. The average log began to be negative starting at T90. |
My favorite gene was RAD53 or YPL153C | My favorite gene was RAD53 or YPL153C | ||
Revision as of 20:02, 23 October 2019
Contents
Electronic Workbook
Purpose
The purpose of this week's lab is to continue off of week 7 by going through the steps of the data life cycle for a DNA microarray dataset
Methods/ Results
Week 8 Interim deadline for excel spreadsheet
How many genes have p < 0.05? and what is the percentage (out of 6189)?
2479/ 6189 or 40%
How many genes have p < 0.01? and what is the percentage (out of 6189)?
1583/ 6189 or 26%
How many genes have p < 0.001? and what is the percentage (out of 6189)?
739/ 6189 or 12%
How many genes have p < 0.0001? and what is the percentage (out of 6189)?
280/6189 or 5%
How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
75/ 6189 or 1.2%
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
1735/ 6189 or 28%
Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?
Unadjusted it is .016
Bonferroni-corrected is 101.3
B-H corrected is .056
What is its average Log fold change at each of the timepoints in the experiment? Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis.
For T15 the average Log was 2.7
For T30 the average Log was 3.3
For T60 the average Log was 3.5
For T90 the average Log was -1.1
For T120 the average Log was -1.8
Does NSR1 change expression due to cold shock in this experiment?
Only at higher time points. The average log began to be negative starting at T90.
My favorite gene was RAD53 or YPL153C
The unadjusted value was .512
Bonferroni-corrected is 3172
B-H corrected is .649
For T15 the average Log was -.5476
For T30 the average Log was -.5768
For T60 the average Log was -.5764
For T90 the average Log was 1.050
For T120 the average Log was -.1536
Data & Files
Conclusion
The purpose of this week's assignment was to go through a DNA microarray dataset and work with filtering p-values that are above or below a specific number. This lab also incorporated STEM which stands for Short Time-series Expression Miner. A Java program used for clustering, comparing, and visualizing short time series gene expression data from microarray experiements.
Acknowledgments
My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We sat together in class to go over the assignment.
References
STEM.Short Time-series Expression Miner. Retrieved on October 23, 2019 from http://www.cs.cmu.edu/~jernst/stem/
LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
Excel Spreadsheet. Retrieved on October 23, 2019 from Excel Spreadsheet
