Difference between revisions of "Ymesfin Week 8"
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#*The data was obtained from the following file: [[Media: Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx| Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx]] | #*The data was obtained from the following file: [[Media: Ymesfin_BIOL367_F19_microarray-data_dHAP4(7846).xlsx| 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. | #*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. | ||
| + | |||
| + | #Performed Statistical Analysis | ||
| + | ##Calculated average results for each datapoint. | ||
| + | ##Calculated Sum square of the entire dataset | ||
| + | ##Created the column headers dHAP4_ss_(TIME) for each timepoint. | ||
| + | ##Calculated Sum Square for each timepoint | ||
| + | ##Calculated Fstat for each data point | ||
| + | ##Calculated p value for each data point | ||
| + | ##Perfomed Bonferroni p value correction for each data point | ||
| + | ##Performed Benjamini & Hochberg p value Correction for each data point | ||
| + | ##Performed Sanity check | ||
==Results== | ==Results== | ||
Revision as of 00:31, 23 October 2019
Purpose
The purpose of this assignment was to create a detailed electronic lab notebook that analyzes a DNA microarray dataset and to demonstrate our understanding of p-value cut-offs.
Methods
- 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.
- Performed Statistical Analysis
- Calculated average results for each datapoint.
- Calculated Sum square of the entire dataset
- Created the column headers dHAP4_ss_(TIME) for each timepoint.
- Calculated Sum Square for each timepoint
- Calculated Fstat for each data point
- Calculated p value for each data point
- Perfomed Bonferroni p value correction for each data point
- Performed Benjamini & Hochberg p value Correction for each data point
- Performed Sanity check
Results
Files
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) 00:26, 16 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 17, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
