Anthony J. Wavrin Week 9: Difference between revisions
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==Assignment 9== | ==Assignment 9== | ||
File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare. | File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare. | ||
1. How many genes have p value < 0.05? | |||
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2. What about p < 0.01? | |||
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3. What about p < 0.001? | |||
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4. What about p < 0.0001? | |||
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5. Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction. | |||
* There were no genes at any time point that has a p value < 0.05 after the Bonferroni correction. | |||
6. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? | |||
* 332 | |||
7. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? | |||
* 212 | |||
8. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? | |||
* 306 | |||
9. How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.) | |||
* 198 | |||
Revision as of 23:09, 2 April 2013
Assignment 9
File of the spreadsheet with the statistics for dHMO1 is uploaded on Lionshare.
1. How many genes have p value < 0.05?
Time | # of genes |
---|---|
15 | 385 |
30 | 544 |
60 | 434 |
90 | 204 |
120 | 190 |
2. What about p < 0.01?
Time | # of genes |
---|---|
15 | 81 |
30 | 108 |
60 | 87 |
90 | 28 |
120 | 34 |
3. What about p < 0.001?
Time | # of genes |
---|---|
15 | 8 |
30 | 10 |
60 | 6 |
90 | 5 |
120 | 4 |
4. What about p < 0.0001?
Time | # of genes |
---|---|
15 | 0 |
30 | 1 |
60 | 1 |
90 | 1 |
120 | 0 |
5. Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
- There were no genes at any time point that has a p value < 0.05 after the Bonferroni correction.
6. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria?
- 332
7. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria?
- 212
8. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
- 306
9. How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.)
- 198
Links
- BIOL398-03/S13
- Anthony J. Wavrin
- Week 2 Journal
- Week 3 Journal
- Week 4 Journal
- Week 5 Journal
- Week 6 Journal
- Week 8 Journal
- Week 9 Journal
- Week 11 Journal
- Week 12 Journal
- Week 13 Journal
- Week 14 Journal
- Week 1 Shared Journal
- Week 2 Shared Journal
- Week 3 Shared Journal
- Week 4 Shared Journal
- Week 5 Shared Journal
- Week 6 Shared Journal
- Week 8 Shared Journal
- Week 9 Shared Journal
- Week 11 Shared Journal
- Week 12 Shared Journal
- Week 13 Shared Journal
- Week 14 Shared Journal
- Anthony J. Wavrin/Matthew E. Jurek Metabolic Pathways Project
- Week 11 Journal Club 2 Slide: Table 1
- Week 13 Journal Powerpoint