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==August 29th== *TO DO TODAY: **Make some slides for Cosmic and CES22k sets to illustrate findings for linear and log fits **Hopefully find a good way to fit normal distributions to the data; create some plots for this **Test CES22k set for proximal and distal bases as well (just as with Dr. Li's data and Cosmic set above) *'''Analysis of Cosmic and CES22k Data Set''' **R^2 value of fit is very low due to large number of data points. ***Idea from Dr. Zhang; check high and low end points for input factors (maybe outside 1 std. deviation?) ***This might increase Signal-to-Noise ratio for the data. **Was doing some reading on R linear model modules; stumbled across ''effects'' module. ***''effects'' uses results from an ''lm'' command and generates "effect plots" ***It generates the effects of a set of variables on an output variable in individual graph form ***Red lines in graphs represent a 95% confidence interval ***A paper on the ''effects'' module can be found here: http://www.jstatsoft.org/v08/i15/paper ***'''Need to investigate this module and make sure that any assumptions it makes are valid for the data we are using.''' ****It seemed that it was being used in a variety of applications online that used linear models. **Used the ''effects'' module on Dr. Zhang's earlier CES22k fit to determine effects of various factors on expression output. ***The results for this are very interesting, and provide a much nicer picture than just the fit data. ---- *'''CES22K SET:'''[[Image:CES22K Effect Plots.png]] ---- *'''COSMIC SET:'''[[Image:Cosmic Effect Plots.png]] ---- *'''Proximal and Distal Arm Base Comparison''' **The above analysis (using [[Media:MakeHist_CES.txt|makeHist_CES.pl]]) was repeated for the CES22k set. **The results are below. {|border="1" cellpadding="5" cellspacing="0" | align="center" colspan="21" | '''CES22k Set Results''' |- |'''Base:'''||A||T||G||C |- |'''Proximal Extension Arm:'''||305.94||326.29||236.49||247.1 |- |'''Distal Extension Arm:'''||283.08||290.35||263.52||257.27 |- |'''Proximal Ligation Arm:'''||244.76||163.81||402.33||253.13 |- |'''Distal Ligation Arm:'''||280.15||303.46||245.07||263.64 |} *[[Image:ProxDist_Base_CES22k.png]] **Similar to Cosmic set results; G and C are preferred at the Proximal Ligation site over A and T. **Differences are more pronounced, like Dr. Li's data. **Some differences are present in the other bases as well...possibly analyze for significance (in Dr. Li's data, Cosmic data, and this data)? *'''Slides to illustrate findings so far''' **Will make tonight (8-29) and email out.
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