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==September 3== *'''TO DO:''' **Analyze arm GC content from CES22K Set and add to Powerpoint. **Add arm length data from CES22K Set and Cosmic Set to Powerpoint. **Implement new scoring system. *'''Data Analysis and [[Media:Cosmic_CES22K_Presentation.ppt|PowerPoint Presentation]]''' **Analyzed arm length from Cosmic set; found that longer arms (on both sides) result in a better capture. ***Will add this to PowerPoint and to scoring. **Need to extract and analyze GC Content from CES22K Set. ***Code to do this is running right now. After this, graphs will be created in R and added to PowerPoint and scoring system. **Turns out arm lengths were normalized to 20 for this set; cannot derive anything from this because of this. **GC results are different; it was found that the ligation arm having a high GC raised expression, while the extension arm having a high GC hurt expression. ***In the Cosmic set, higher GC in either arm led to decreased expression. ***I am not sure why this is the case; look into how probes were constructed for tips. *'''New Scoring System''' **For scoring, intercept of fit does not really matter, since all scores are just going to be compared to each other. We therefore just need to apply the slope. **New Score: ***p_score = m_LTm * Left_Tm + m_RTm * Right_Tm + m_LUnique * L_Unique + m_RUnique * R_Unique + m_TLength * T_Length + m_LLength * L_Length + m_RLength * R_Length + m_LGC * GC_Content_Left + m_RGC * GC_Content_Right + proxLigFactor **This scoring should produce much better probes than previous iterations, as all of these factors will be fitted. **Additional factors can then be analyzed as well. **Added new scoring system to GetCpGProbes.pl file. Just need to decide exactly which slopes to use for probe scoring. ***Will probably average results from Cosmic and CES22K (after making sure that other factors didn't cause differences; if this is the case, a weighted average will be used).
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