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=== Round 4: Check the Batch 1 and Batch 2 samples=== * Dr.Zhang found the signficant difference between batch 1 and batch 2 samples. * Dinh check the difference between phase I and phase II samples - **(1) bisulfite conversion rate (quantified by Lambda DNA spike-in) were between 98.54%-99.40% for phase I and lower between 96.61%-98.63% for phase II. **(2) According to Noi's wikinotes, the ChargeSwitch gDNA serum kit was used to extract DNA from plasma in phase I and we used QIAmp plasma nucleic acid kit in phase II. * Then how about the methylation level difference between batch 1 and batch 2 ** Select same loci check the methylation level difference between batch 1 and batch 2 ** Use same loci to do the clust analysis. ** Do we have clinical information to the samples? ** Dinh found no batch effect between phase 1 and phase 2 as the following. cd /home/shg047/monod/mixHap/hapinfo/ Rscript [[methylationlevel_MHL_batch1_batch2.R]] *[[File:32E9.tm.png|1000x400px]] * box-plot for all the samples is as the following (methylation level) *[[File:199.tm.png|400px]] * Density plot is as the following(methylation level): *[[File:DF.tm.png|400px]] *MHL Difference between Batch 1 and Batch 2 sets *[[File:3573.tm.png|400px]] *# genome-miner cd /home/shg047/monod/hapinfo less -S 6-P-1.hapInfo.txt less -S 6-P-11.hapInfo.txt *Obviously, the distribution of the methylation status in the reads caused such difference. *[[File:3A97.tm.png|400px]] *Question: Is there any golden standard RRBS/prior distribution for cancer plasma??
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