Msamdars Week 8
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Contents
Purpose
Methods/Results
- Strain: Saccharomyces cerevisiae - Δcin5 deletion strain
- My Filename: BIOL367_F19_dCIN5_MS.xlsx
- Replicates: 4 replicates for each timepoint
- Timepoints: t15, t30, t60, t90, t120
Data & Files
Zip file containing Excel sheet post-sanity check and STEM .txt file
Sanity Check
- How many genes have p < 0.05? and what is the percentage (out of 6189)?
- 2290 out of 6189 or 37.00% of the 6189 genes.
- How many genes have p < 0.01? and what is the percentage (out of 6189)?
- 1380 out of 6189 or 22.30% of the 6189 genes.
- How many genes have p < 0.001? and what is the percentage (out of 6189)?
- 691 out of 6189 or 11.16% of the 6189 genes.
- How many genes have p < 0.0001? and what is the percentage (out of 6189)?
- 358 out of 6189 or 5.784% of the 6189 genes.
- How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
- 151 out of 6189 or 2.440% of the 6189 genes.
- How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
- 1453 out of 6189 or 23.48% of the 6189 genes.
Summary slide with statistics about microarray data.
Conclusion
This week we continued the analysis of our data. This data was processed and corrected using commonly used techniques, taking the average log-fold change, performing a t-test on that data, calculating that using Bonferroni method, and doing a second correction using the Benjamini and Hochberg method. I then also prepared to load that data into the STEM software.
Acknowledgments
This week my team members included Emma Young, Ivy-Quynh Macaraeg, & DeLisa Madere. We worked in class together.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Other Links
| Links | ||
|---|---|---|
| Mihir Samdarshi User Page | ||
| Assignment Pages | Personal Journal Entries | Shared Journal Entries |
| Week 1 | Journal Week 1 | Class Journal Week 1 |
| Week 2 | Journal Week 2 | Class Journal Week 2 |
| Week 3 | FAS2/YPL231W Week 3 | Class Journal Week 3 |
| Week 4 | Journal Week 4 | Class Journal Week 4 |
| Week 5 | Database - AmtDB | Class Journal Week 5 |
| Week 6 | Journal Week 6 | Class Journal Week 6 |
| Week 7 | Journal Week 7 | Class Journal Week 7 |
| Week 8 | Journal Week 8 | Class Journal Week 8 |
| Week 9 | Journal Week 9 | Class Journal Week 9 |
| Assignment Pages | Personal Journal Entries | |
| Week 10 | Journal Week 10 | |
| Week 11 | Journal Week 11 | |
| Week 12/13 | Journal Week 12/13 | |
| Team Project Links | ||
| Skinny Genes Team Page | ||
References
- LMU BioDB 2019. (2019). Week 8. Retrieved October 15, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
- MediaWiki (2019). Category: Help. Retrieved October 15, 2019, from https://www.mediawiki.org/wiki/Category:Help
