Ns126:Calendar/NOTES/2015-7-12: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Shicheng
>Shicheng
Line 10: Line 10:
===Relationship between samples in the propestive of hierarchical clustering based on MHL===
===Relationship between samples in the propestive of hierarchical clustering based on MHL===


  N37<-("Colon","Frontal lobe","Heart","Small intestine","Liver","Lung","Skeletal muscle","Pancrease","Stomach")
  N37<-c("Colon","Frontal lobe","Heart","Small intestine","Liver","Lung","Skeletal muscle","Pancrease","Stomach")


<gallery widths=800px heights=400px>
<gallery widths=800px heights=400px>

Revision as of 17:28, 16 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

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")
  • consider: batch differences in read depth, read length or other artifacts.

Relationship between samples in the propestive of PCA analysis based on MHL

File:WGBS.MONOD.PCA.2.jpeg

Functional enrichment of the loci that have the highest loading to PC1 and PC2

Methylation 450K sample with CD, ESC and Cancer sample in the sapce of PC1 and PC2