Difference between revisions of "Sulfiknights DA Week 12/13"
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===Conducting the ANOVA=== | ===Conducting the ANOVA=== | ||
| − | Sanity Check: 1068/4785 p-values are less than 0.05 | + | *All data analysis was conducted on data on the "GSE6068_setA_family" sheet. |
| + | *ANOVA procedure was based on the methods from [[Week 8]]. | ||
| + | #A new sheet called "swtVnwt_1mM_ANOVA" was created and all data from Columns A-R was copied and pasted into this sheet. | ||
| + | #Columns "swtVnwt_AvgLogFC_1mM_15m" - "swtVnwt_AvgLogFC_1mM_1080m" for each time point 15m, 30m, 60m, and 1080m were created and contain the equation the average of each replicate for each time point. | ||
| + | #Column "swtVnwt_ss_HO" was created containing the equation SUMSQ(D2:R2). | ||
| + | #Sanity Check: 1068/4785 p-values are less than 0.05 | ||
==Data & Files== | ==Data & Files== | ||
Revision as of 17:23, 25 November 2019
| Sulfiknight Links | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| BIOL Databases Main Page | Sulfiknights: Project Overview Page | Final Project Deliverables Requirements | Sulfiknights: Final Project Deliverables | Members | Project Manager & Quality Assurance: Naomi Tesfaiohannes | Quality Assurance: Joey Nimmers-Minor | Data Analysis: Ivy-Quynh Macaraeg & Marcus Avila | Designer: DeLisa Madere | |
| Assignment Pages | Week 11 | Week 12/13 | Week 15 | ||||||
Contents
Purpose
Methods & Results
Sample to data relationship table:
- GSE6068_setA_family - swt vs nswt 1mM @ 1 hr (6 replicates); 15 min, 30 min, 18 hrs (3 replicates each)
- GSE6129_set0_family - swt vs nswt 1mM @ 1hr; 6 replicates
- GSE6129_set1_family - swt vs nswt .2mM @ 1 hr, 15 min, 30 min, 18 hr; 3 replicates each
- GSE6129_set2_family - sYAP4 vs swt .2mM AND 1 mM each @ 1 hr, 3 replicates each
- GSE6129_set3_family - sMET4 vs swt .2mM AND 1 mM each @ 1 hr, 3 replicates each
Organizing the Data
- Downloaded data from Thorsen et al.
- Changed "Name" to "Standard_ID" in column C.
- Names were changed to the standard names by the "ORF List <-> Gene List" tool from YEASTRACT.
- Changed column headers in each sheet:
- swt = stressed wild type, nswt= nonstressed wild type
- 1mM, 0.2mM = concentration of As(III) at which the cell was exposed
- 1h, 15m, 30m, 18h = time point (h = hours, m = minutes)
- rn = replicate number (n)
- Inserted MasterIndex in "GSE6068_setA_family"sheet.
Conducting the ANOVA
- All data analysis was conducted on data on the "GSE6068_setA_family" sheet.
- ANOVA procedure was based on the methods from Week 8.
- A new sheet called "swtVnwt_1mM_ANOVA" was created and all data from Columns A-R was copied and pasted into this sheet.
- Columns "swtVnwt_AvgLogFC_1mM_15m" - "swtVnwt_AvgLogFC_1mM_1080m" for each time point 15m, 30m, 60m, and 1080m were created and contain the equation the average of each replicate for each time point.
- Column "swtVnwt_ss_HO" was created containing the equation SUMSQ(D2:R2).
- Sanity Check: 1068/4785 p-values are less than 0.05
Data & Files
Conclusion
Acknowledgments
References
- Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006
