Vkuehn Week 15

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