Difference between revisions of "Ntesfaio Week 8"
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'''Week 8 Interim deadline for excel spreadsheet''' | '''Week 8 Interim deadline for excel spreadsheet''' | ||
| − | [[ | + | [[Media:BIOL367 F19 microarray-data dHAP4NtesfaioNT.xlsx| Excel Spreadsheet]] |
How many genes have p < 0.05? and what is the percentage (out of 6189)? | How many genes have p < 0.05? and what is the percentage (out of 6189)? | ||
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For T120 the average Log was -1.8 | For T120 the average Log was -1.8 | ||
| − | Does NSR1 change expression due | + | Does NSR1 change expression due to cold shock in this experiment? |
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My favorite gene was RAD53 or YPL153C | My favorite gene was RAD53 or YPL153C | ||
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[[Media:BIOL367 F19 sample p-value slideNtesfaio.pptx| Powerpoint Slide]] | [[Media:BIOL367 F19 sample p-value slideNtesfaio.pptx| Powerpoint Slide]] | ||
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| + | [[Media:NtesfaioSTEM profiling.pdf| Stem Profile]] | ||
===Conclusion=== | ===Conclusion=== | ||
| + | The purpose of this week's assignment was to go through a DNA microarray dataset and work with filtering p-values that are above or below a specific number. This lab also incorporated STEM which stands for Short Time-series Expression Miner. A Java program used for clustering, comparing, and visualizing short time series gene expression data from microarray experiements. | ||
===Acknowledgments=== | ===Acknowledgments=== | ||
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===References=== | ===References=== | ||
| + | STEM.Short Time-series Expression Miner. Retrieved on October 23, 2019 from http://www.cs.cmu.edu/~jernst/stem/ | ||
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{{Template:Ntesfaio}} | {{Template:Ntesfaio}} | ||
Revision as of 10:55, 23 October 2019
Contents
Electronic Workbook
Purpose
The purpose of this week's lab is to continue off of week 7 by going through the steps of the data life cycle for a DNA microarray dataset
Methods/ Results
Week 8 Interim deadline for excel spreadsheet
How many genes have p < 0.05? and what is the percentage (out of 6189)?
2479/ 6189 or 40%
How many genes have p < 0.01? and what is the percentage (out of 6189)?
1583/ 6189 or 26%
How many genes have p < 0.001? and what is the percentage (out of 6189)?
739/ 6189 or 12%
How many genes have p < 0.0001? and what is the percentage (out of 6189)?
280/6189 or 5%
How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
75/ 6189 or 1.2%
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
1735/ 6189 or 28%
Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values?
Unadjusted it is .016
Bonferroni-corrected is 101.3
B-H corrected is .056
What is its average Log fold change at each of the timepoints in the experiment? Note that the average Log fold change is what we called "STRAIN)_AvgLogFC_(TIME)" in step 3 of the ANOVA analysis.
For T15 the average Log was 2.7
For T30 the average Log was 3.3
For T60 the average Log was 3.5
For T90 the average Log was -1.1
For T120 the average Log was -1.8
Does NSR1 change expression due to cold shock in this experiment?
My favorite gene was RAD53 or YPL153C
The unadjusted value was .512
Bonferroni-corrected is 3172
B-H corrected is .649
For T15 the average Log was -.5476
For T30 the average Log was -.5768
For T60 the average Log was -.5764
For T90 the average Log was 1.050
For T120 the average Log was -.1536
Data & Files
Conclusion
The purpose of this week's assignment was to go through a DNA microarray dataset and work with filtering p-values that are above or below a specific number. This lab also incorporated STEM which stands for Short Time-series Expression Miner. A Java program used for clustering, comparing, and visualizing short time series gene expression data from microarray experiements.
Acknowledgments
My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We sat together in class to go over the assignment.
References
STEM.Short Time-series Expression Miner. Retrieved on October 23, 2019 from http://www.cs.cmu.edu/~jernst/stem/
