Difference between revisions of "Vkuehn Week 15"
From LMU BioDB 2013
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**Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue''' | **Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored '''blue''' | ||
**Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple''' | **Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored '''purple''' | ||
| + | ===GenMAPP Finder=== | ||
| + | ran genmapp and waiting for results to be generated | ||
Revision as of 18:48, 5 December 2013
Contents |
ELECTRONIC NOTEBOOK
12/5/13
Sanity Check
- P-value less than 0.05: 5303
- P-value less that 0.01: 2130
- P-value less that 0.001: 317
- P-value less that 0.0001: 0
- Out of the 19201 T tests performed, more than 960 results had a P-value less than 0.05. Since 5303 genes passed this cut off it means that there were some significant changes.
- Keeping the "Pvalue" filter at p < 0.05, filter the "Avg_LogFC" column to show all genes with an average log fold change greater than zero. These were the ones that increased relative to control. There were 2970
- Genes with an average log fold change less than zero. These were the ones that decreased relative to control. There were: 2334
- Average log fold change of > 0.25 and p < 0.05: 2861
- Average log fold change of < -0.25 and p < 0.05: 2431
GenMAPP Expression Dataset Manager
- For exact procedure reference [Vkuehn Week 13] or the procedure from http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols
- The colors were assigned to the two main criterion
- Increased relative to control had a Log FC> 0.25 and P-Value <0.05 these were colored blue
- Decreased relative to control had a Log FC< -0.25 and P-Value <0.05 these were colored purple
GenMAPP Finder
ran genmapp and waiting for results to be generated
