Anthony J. Wavrin Week 9: Difference between revisions
(added qs 5-8 with answers) |
(added question 9 and 10 with answers) |
||
Line 77: | Line 77: | ||
* 198 | * 198 | ||
10.Find NSR1 in your dataset. Is it's expression significantly changed at any timepoint? Record the average fold change and p value for NSR1 for each timepoint in your dataset. | |||
* There were no time points that had "significiantly" changed but, some time points were close to a p value of 0.05. | |||
{| border="1" class="wikitable" | |||
|- | |||
! Time !! Avg Fold Change !! P Value | |||
|- | |||
| 15 || 0.91 || 0.0385 | |||
|- | |||
| 30 || 1.19 || 0.0722 | |||
|- | |||
| 60 || 1.26 || 0.1618 | |||
|- | |||
| 90 || -0.24 || 0.5704 | |||
|- | |||
| 120 || -0.25 || 0.5507 | |||
|} | |||
[[BIOL398-03/S13:Week_9| Original Assignment]] | [[BIOL398-03/S13:Week_9| Original Assignment]] | ||
{{template:Anthony J. Wavrin}} | {{template:Anthony J. Wavrin}} |
Revision as of 23:13, 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
10.Find NSR1 in your dataset. Is it's expression significantly changed at any timepoint? Record the average fold change and p value for NSR1 for each timepoint in your dataset.
- There were no time points that had "significiantly" changed but, some time points were close to a p value of 0.05.
Time | Avg Fold Change | P Value |
---|---|---|
15 | 0.91 | 0.0385 |
30 | 1.19 | 0.0722 |
60 | 1.26 | 0.1618 |
90 | -0.24 | 0.5704 |
120 | -0.25 | 0.5507 |
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