Difference between revisions of "Knguye66 Week 7"
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(→Microarray Data Analysis (wild type data): add questions) |
(→Sanity Check: add qs) |
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==== Sanity Check ==== | ==== Sanity Check ==== | ||
| − | * The number of genes that are significantly changed at p value cut-off of p < 0.05 | + | * The number of genes that are significantly changed at p value cut-off of p < 0.05: |
** 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)? | ||
** How many genes have p < 0.01? and what is the percentage (out of 6189)? | ** How many genes have p < 0.01? and what is the percentage (out of 6189)? | ||
| Line 19: | Line 19: | ||
* How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)? | * How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)? | ||
* How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)? | * How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)? | ||
| + | |||
| + | * Comparing results with known data: | ||
| + | ** Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment? | ||
Revision as of 14:11, 15 October 2019
Contents
Microrray Data Analysis (wild type data)
Background
Part 1: Statistical Analysis Part 1
Bonferroni and p value Correction
Benjamini & Hochberg p value Correction
Sanity Check
- The number of genes that are significantly changed at p value cut-off of p < 0.05:
- How many genes have p < 0.05? and what is the percentage (out of 6189)?
- How many genes have p < 0.01? and what is the percentage (out of 6189)?
- How many genes have p < 0.001? and what is the percentage (out of 6189)?
- How many genes have p < 0.0001? and what is the percentage (out of 6189)?
- How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
- How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
- Comparing results with known data:
- Find NSR1 in your dataset. What is its unadjusted, Bonferroni-corrected, and B-H-corrected p values? What is its average Log fold change at each of the timepoints in the experiment?
