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==August 27th== *Have code to read and analyze Cosmic set data; file is [[Media:ReadCosmic_20080827.txtβ|"readCosmic.pl"]] *'''Comparison of Cosmic set data to Dr. Li's data (Harvard Collaborator)''' **Dr. Li's data showed that the last base pair of the ligation arm was important. ***Dr. Li checked average expression for each base. ***G was preferred for ligation, followed by A, C, and T. ***[[Image:08_22_2008_JinLi_Ligation_Arm_Base_Dist.png]] **Average expression was calculated using the [[Media:MakeHist_20080827.txt|"makeHist.pl"]] file. ***This file averages the abundance of the probes that used each base. **The results were slightly different. ***For the COSMIC set, it was found that for the proximal ligation arm, G was preferred, followed by C, A, and T. ***This makes intuitive sense, as the bond between G and C is stronger than the bond between A and T. ***The results were also much less pronounced than Dr. Li's results; the difference in base performance is much smaller. {|border="1" cellpadding="5" cellspacing="0" | align="center" colspan="21" | '''Cosmic Set Results''' |- |'''Base:'''||A||T||G||C |- |'''Proximal Extension Arm:'''||98.2276826484018||105.4814504701790||97.8751164168995||105.1120477176380 |- |'''Distal Extension Arm:'''||104.9745183977170||107.4126226040130||106.5526921141540||88.8525735059634 |- |'''Proximal Ligation Arm:'''||95.1374247734938||83.7531848897751||135.360909000299||107.876484056988 |- |'''Distal Ligation Arm:'''||103.1547820103830||113.0664396095970||96.5690024678530||96.7110820814283 |} *[[Image:ProxDist_Base_Cosmic.png]] **Analyze these results later; perhaps add in a preference on the Proximal Ligation Arm to favor G or C over A or T in the score. *'''Implementation of new probe set algorithm.''' **Algorithm is summarized above. **Implement in Perl using hash table in getCpGIslands.pl file. *'''Use R to analyze Cosmic Data Set''' ** Downloaded and installed GNU R and R-commander (GUI) ***Can load CSV and tab-separated files. **''lm'' command can do a linear model fit to the data. ***May need to take the log of several pieces of data however in order to improve fit (if data is exponentially correlated). ***Initial ''lm'' results for Cosmic set show a very poor correlation...probably need to take log of several pieces of data set. **Earlier, Dr. Zhang's analysis on CES22K set used the following factors: ***ProbeDist: distribution of oligo abundance determined by Solexa sequencing. - '''Don't have this for the Cosmic set''' ***H1_Tm, H2_Tm: H1 (ligation arm), H2 (extension arm), 12bp sub-sequences of H1 and H2. - '''Normalized for the Cosmic set; very close to 62 C in all cases''' ***H1R_dist, H2L_dist: K-mer distribution of H1&H2 12bp sub-sequences in the human genome. - '''Have this''' ***Core_25bp_genomic_homology: weighted score of the 25bp homologous sequences in the human genome, mapped by SOAP with <=3bp mismatches. - '''Not sure what this is...ask Dr. Zhang'''
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