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===results=== used previously published WGBS on ES cell cultured under 2i and serum conditions [http://www.sciencedirect.com/science/article/pii/S1934590913002609 Link] do BSmooth on all the data: ns=20 and h=2000 (20 CpG sites in the window that range from minimum =2000 and maximum =10,000) then run Tstat to do the comparison: SCNT-serum (indx 9 and 10) against ES-serum (indx11 and Habibi_ES_serum) (ES serum is group2 and also used to estimate variability) iPSC-serum (indx 1, 2, 4, 5) against ES-serum (indx11 and Habibi_ES_serum) (ES serum is group2 and also used to estimate variability) SCNT-2i (indx 6 and 7) against ES-serum (Habibi_ES_2i_adapted and Habibi_ES_2i) (ES 2i is group2 and also used to estimate variability) Among the candidate DMRs generated from the above steps, we were able to detect true culture-specific DMRs, where there are differentially methylated regions between 2i and serum conditions. However, because this method relies on biological replicates to do smoothing and calculate T-statistics, so we have decided to use other published method to find DMRs.
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