Ymesfin Week 8

Purpose

The purpose of this assignment was to create a detailed electronic lab notebook to statistically analyze a DNA microarray dataset and to demonstrate our understanding of p-value cut-offs.

Week 7 Assignment

Week 8 Assignment

Methods

1. The data was first downloaded from the wiki
   • The strain we will be analyzing is Delta-Hap4
   • The data was obtained from the following file: Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx
   • The file had timepoints at 15, 30, 60, 90, and 120 minutes. All the timepoints had 4 replicates but the 90 and 120 minute timepoints had 3 replicates. There were a total of 6189 samples in this dataset.
2. Performed ANOVA Statistical Analysis
   1. Calculated average results for each datapoint.
   2. Calculated Sum square of the entire dataset
   3. Created the column headers dHAP4_ss_(TIME) for each timepoint.
   4. Calculated Sum Square for each timepoint
   5. Calculated Fstat for each data point
   6. Calculated p value for each data point
   7. Perfomed Bonferroni p value correction for each data point
   8. Performed Benjamini & Hochberg p value Correction for each data point
   9. Performed Sanity check
3. Clustering and GO Term Enrichment with STEM Software

Results

Files

dHAP4 Data Sheet

dHAP4 stem data

P Values and Stem Results

Ymesfin

Main Page

Ymesfin

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Skinny Genes

Week 12

Week 13

Week 14

Week 15

Acknowledgements

Dr. Kam Dahlquist; Professor

Naomi Tesfaiohannes; Homework Partner

David Ramirez; Homework Partner

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

Ymesfin (talk) 01:32, 23 October 2019 (PDT)

References

LMU BioDB 2019. (2019). Week 7. Retrieved October 16, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_7

LMU BioDB 2019. (2019). Week 8. Retrieved October 23, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8