Noi/NOTES/2012-4-6: Difference between revisions
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* 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). | * 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. | * Note: I will add more information about analysis and PCA analysis result after removing CpG sites with less confident. | ||
[[File:UCLA-GA_age_t2.5_p.png| | A=read.table("clean_UCLA-GA_age_t2.5_methylMatrix.txt", header=TRUE,row.names=1) | ||
[[File:UCLA-GA_disease_t2.5_p.png| | B=na.omit(A) | ||
[[File:UCLA-GA_sex_t2.5_p.png| | B$STDEV=NULL | ||
B$min_RD=NULL | |||
B$mean_RD=NULL | |||
str(B) | |||
'data.frame': '''650 obs.''' of 169 variables: | |||
pca_sites <- prcomp(B, scale=TRUE) | |||
summary(pca_sites) | |||
PC1 PC2 PC3 PC4 PC5 PC6 PC7 | |||
Proportion of Variance 0.662 0.0391 0.0128 0.00835 0.00799 0.00715 0.00597 | |||
pca1 <- prcomp(t(B), scale=TRUE) | |||
summary(pca1) | |||
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 | |||
Proportion of Variance 0.128 0.0551 0.029 0.0231 0.0185 0.0171 0.0152 0.0139 | |||
[[File:UCLA-GA_age_t2.5_p.png| 800px]] | |||
[[File:UCLA-GA_disease_t2.5_p.png| 800px]] | |||
[[File:UCLA-GA_sex_t2.5_p.png| 800px]] |
Revision as of 18:46, 17 April 2012
- Link to calendar: [[1]]
Regression analysis of UCLA SZ data set
- Continued from http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-1 and after getting comments from Dr. Zhang during lab meeting (2012_04_04)
- From the list of CpG sites from regression analysis. I performed PCA analysis again by adding the GA samples from Kang Zhang's lab as control (only the 73 good quality samples).
- Note: I will add more information about analysis and PCA analysis result after removing CpG sites with less confident.
A=read.table("clean_UCLA-GA_age_t2.5_methylMatrix.txt", header=TRUE,row.names=1) B=na.omit(A) B$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