Difference between revisions of "Ntesfaio Week 8"
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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. | 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 | + | For T15 the average Log was 2.7 |
| − | For T30 the average Log was 3. | + | For T30 the average Log was 3.3 |
| − | For T60 the average Log was 3. | + | For T60 the average Log was 3.5 |
| − | For T90 the average Log was | + | For T90 the average Log was -1.1 |
| − | For T120 the average Log was | + | For T120 the average Log was -1.8 |
Does NSR1 change expression due | Does NSR1 change expression due | ||
to cold shock in this experiment? | 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=== | ===Data & Files=== | ||
Revision as of 20:14, 22 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
File:Copy of BIOL367 F19 microarray-data dHAP4NtesfaioNT.zip
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
Media:Copy of BIOL367 F19 microarray-data dHAP4NtesfaioNT.zip
Conclusion
Acknowledgments
My homework partners this week are Aby User:Ymesfin and David User:Dramir36. We sat together in class to go over the assignment.
