Analysis of batch vs clinical traits
Number of clinical traits: 23
Number of batches based on the pattern for DNA methylation samples: 3
Correlation between batch and center in AML:
> table(batchID,two)
two
batchID AB
0741 96
0742 73
0743 25
There is only one center from which all patients come from.
Significant trait - batch correlations (all other correlations can be found in a table here)
"LAML_clinical_traits","DataType","NumberOfNAs","Test","Pvalue"
"days_to_form_completion","integer",2,"Kruskal-Wallis rank sum test",1.22E-26
"year_of_initial_pathologic_diagnosis","integer",2,"Kruskal-Wallis rank sum test",2.53E-26
"days_to_death","integer",82,"Kruskal-Wallis rank sum test",3.94E-04
"prior_diagnosis","factor",2,"Pearson's Chi-squared test",1.63E-03
"vital_status","factor",2,"Pearson's Chi-squared test",5.25E-03
"age_at_initial_pathologic_diagnosis","integer",2,"Kruskal-Wallis rank sum test",1.66E-02
"days_to_birth","integer",2,"Kruskal-Wallis rank sum test",1.90E-02
"hydroxyurea_administration_prior_registration_clinical_study_indicator","factor",2,"Pearson's Chi-squared test",3.05E-02
"pretreatment_history","factor",2,"Pearson's Chi-squared test",3.05E-02