Noi/NOTES/2012-4-6

From ZhangLabWiki
Revision as of 18:46, 17 April 2012 by >Noi
Jump to navigation Jump to search
  • Link to calendar: [[1]]

Regression analysis of UCLA SZ data set

  • Continued from http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-1 and after getting comments from Dr. Zhang during lab meeting (2012_04_04)
  • From the list of CpG sites from regression analysis. I performed PCA analysis again by adding the GA samples from Kang Zhang's lab as control (only the 73 good quality samples).
  • Note: I will add more information about analysis and PCA analysis result after removing CpG sites with less confident.
A=read.table("clean_UCLA-GA_age_t2.5_methylMatrix.txt", header=TRUE,row.names=1)
B=na.omit(A)
B$STDEV=NULL
B$min_RD=NULL
B$mean_RD=NULL
str(B)
'data.frame':	650 obs. of  169 variables:
pca_sites <- prcomp(B, scale=TRUE)
summary(pca_sites)
                        PC1    PC2    PC3     PC4     PC5     PC6     PC7
Proportion of Variance  0.662 0.0391 0.0128 0.00835 0.00799 0.00715 0.00597
pca1 <- prcomp(t(B), scale=TRUE)
summary(pca1)
                        PC1    PC2   PC3    PC4    PC5    PC6    PC7    PC8
Proportion of Variance 0.128 0.0551 0.029 0.0231 0.0185 0.0171 0.0152 0.0139
File:UCLA-GA age t2.5 p.png 

File:UCLA-GA disease t2.5 p.png File:UCLA-GA sex t2.5 p.png