Ns126:Calendar/NOTES/2015-7-12: Difference between revisions
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File:RRBS.Boxplot.pahse2.jpeg|Figure 1C. Boxplot for the distribution of MHL in RRBS dataset | File:RRBS.Boxplot.pahse2.jpeg|Figure 1C. Boxplot for the distribution of MHL in RRBS dataset | ||
File:SeqCap.phase2.boxplot.jpeg|Figure 1D. Boxplot for the distribution of MHL in SeqCap dataset | File:SeqCap.phase2.boxplot.jpeg|Figure 1D. Boxplot for the distribution of MHL in SeqCap dataset | ||
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Revision as of 07:05, 21 July 2015
Materials and Method
Dr. Zhang update the MONOD methylation haplotype result and therefore I can check the latest result in the relationship between samples and check the distinguish ability of cancer and normals based on methylation haplotype load.
About the data processing, check: http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/MONOD/2015-7-6
Result
MHL Distrbution in 3 dataaset
- WGBS.Boxplot.phase2.withcancer.jpeg
Figure 1A-1. Boxplot for the distribution of MHL in WGBS dataset(total)
- WGBS.Boxplot.phase2.jpg.jpeg
Figure 1A-2. Boxplot for the distribution of MHL in WGBS dataset(part)
- RRBS.Boxplot.pahse2.jpeg
Figure 1C. Boxplot for the distribution of MHL in RRBS dataset
- SeqCap.phase2.boxplot.jpeg
Figure 1D. Boxplot for the distribution of MHL in SeqCap dataset
Relationship between samples in the propestive of hierarchical clustering based on MHL
N37<-c("Colon","Frontal lobe","Heart","Small intestine","Liver","Lung","Skeletal muscle","Pancrease","Stomach") N37<-c("LymphNodes","Blood","Colon","BrainCRBM","Heart","Liver","Lung","Muscle","Pancreas","Stomach") # modified
- WGBS.Hclust.Complete.phase2.jpeg
Figure 1A. Hierarchical clustering based on WGBS revealed the relationships between hESC, N37 normals, Salk normals and cancers
- consider: batch differences in read depth, read length or other artifacts.
- RRBS.PhaseI.Cluster.Revise.jpeg
Figure 1B. Hierarchical clustering based on RRBS revealed the relationships between Plasma, Nomal and Cancer tissues.
- SeqCap.Phase2.Cluster.Revised.jpeg
Figure 1C.Hierarchical clustering based on SeqCap revealed the relationships between Plasma, Nomal and Cancer tissues.