Knguye66 Week 9

Microrray Data Analysis (wild type data)

Purpose

This week's assignment is to continue the Microarray Data Anaylsis for wild type data. Step 4 and 5 from Week 9 are featured: Viewing and Saving STEM results, and Analyzing and Interpreting STEM results. For reference and files, go to: knguye66 Week 8.

Methods/Results

After finishing the steps on Week 8 for Statistical Analysis Part I: ANOVA on Microsoft Excel, a quick sanity check was performed for the p-value dataset. Following the filtering of the data, with a p-value of less than 0.05, 2528 of 6189 records were found. This means, in a p-value of less than 0.05, there is a 5% chance that 2528 out of 6189 records would be found.

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Sanity Check Questions:

-Unadjusted p-value-

1. How many genes have p<0.05? and what is the percentage (out of 6189)?
   • 2528, 40.8%
2. How many genes have p<0.01? and what is the percentage (out of 6189)?
   • 1652, 26.7%
3. How any genes have p<0.001? and what is the percentage (out of 6189)?
   • 919, 14.8%
4. How many genes have p<0.0001? and what is the percentage (out of 6189)?
   • 496, 8.0%

-Bonferroni & Benjamini and Hochberg p-value-

1. How any genes are p<0.05 for the Bonferroni-corrected p-value? and what is the percentage (out of 6189)?
   • 248, 4.0%
2. How any genes are p <0.05 for the Benjamini and Hochberg-corrected p-value? and what is the percentage (out of 6189)?
   • 1822, 29.4%

-NSR1-

1. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p-values?
   • Unadjusted: 2.86939E-10
   • Bonferroni: 1.77586E-06
   • B-H: 8.87932E-07
   • Average Log fold:
     • t15: 3.279225
     • t30: 3.621
     • t60: 3.526525
     • t90: -2.04985
     • t120: -0.60622

-Favorite Gene (YDR090C)-

1. • Unadjusted: 0.519632074
   • Bonferroni: 3216.002905
   • B-H: 0.641276751
   • Average Log fold:
     • t15: -0.067
     • t30: 0.51286
     • t60: 0.5417
     • t90: -0.27156
     • t120: -0.06704

Data and Files

• [[Media: Wt_genelist_kn.zip | Profile Genelist (zip file)

Acknowledgements

This section is in acknowledgement to partner Christina Dominguez (User:Cdomin12), as well as, Marcus Avila (User:Mavila9) and Jonar Cowan (User:Jcowan4). I would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

User Page

User:knguye66

Template Page

Template:knguye66

Table of all assignments and journal entries for BIO-367-01

Week	Individual Journal Entry	Shared Journal
Week 1	-	Class Journal Week 1
Week 2	knguye66 Week 2	Class Journal Week 2
Week 3	ILT1/YDR090C Week 3	Class Journal Week 3
Week 4	knguye66 Week 4	Class Journal Week 4
Week 5	DrugCentral Week 5	Class Journal Week 5
Week 6	knguye66 Week 6	Class Journal Week 6
Week 7	knguye66 Week 7	Class Journal Week 7
Week 8	knguye66 Week 8	Class Journal Week 8
Week 9	knguye66 Week 9	Class Journal Week 9
Week 10	knguye66 Week 10	Class Journal Week 10
Week 11	knguye66 Week 11	FunGals
Week 12/13	knguye66 Eyoung20 Week 12/13	FunGals
Week 15	knguye66 Eyoung20 Week 15	Class Journal Week 15

References

• GEO Accession viewer. (n.d.). Retrieved from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83656.
• Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 11:14, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8