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== Discussion with Dr. Zhang == * After discussing with Dr. Zhang, he seems to like the idea of using T-test to characterize a significant ASM rather than binomial test since the significant sites tend to show a consistency of sequence preference DNA methylation. * He also suggested to calculate FDR with the two options (FDR < 20% is still acceptable, but <5% is ideal) ** Using MULTTest (R) ** Calculate FDR = (N * p-value cutoff)/M, N = number of CpG sites have been tested, M = number of significant CpG site derived from the test at p-value cutoff *** I have calculate FDR, p-value cutoff 0.05 -->(73,271 * 0.05)/9,123 = 40.1% FDR (this number seem to be very high FDR) p-value cutoff 0.01 -->(73,271 * 0.01)/8,281 = 8.8% FDR p-value cutoff 0.02 -->(73,271 * 0.02)/8,563 = 17.1% FDR *** I will try to calculate FDR by MULTTest function in R * Another suggestion from him is to plot the graph between -log(p-value) vs. the distance between SNP and CpG (for those site of SNP-free CpG), and see the trend of the graph. * More details for suggestions for mpo-mQTL-ASM analysis: Dr. Zhang suggested to generated Ven diagram to see the overlapping of CpG sites from three analyses. * Another issue is make sure that the SNP and CpG coordinates are consistent since this could affect the number of SNP-free and SNP-containing CpG on ASM analysis. ** 2012_03_26 Check the coordinates of SNP and CpG showing ASM on genome browser. Ex. Chr5:43194137(SNP):43194136(CpG) for CpG position if SNP and CpG were assigned on the same coordinate (both start position (0) or both stop position (1), CpG should show C while SNP should show any sequence A G T or C, but not always the same sequence as CpG. Otherwise it is likely that CpG is assigned as1 and SNP is assigned as 0 coordinate. ** After checking multiples SNP-CpG pairs, I am pretty sure that their coordinates were consistent. Ex. Chr5:43194137(SNP) --> G:43194136(CpG) --> C, Chr4:5990551(SNP)--> G:5990550(CpG) --> C, Chr9:139000412(SNP) --> C :139000411 --> C, Chr1:26485013(SNP) --> T :26485012(CpG) --> C ** Also if SNP is on CpG it should show the same sequence. Ex. Chr15:100104385(SNP) --> C :100104385(CpG) --> C, Chr11:17461329(SNP) --> C :17461329(CpG) --> C
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