Page Comparison

h5. Batch vs clinical traits

Number of batches is 12. Correlation between batch and center:
{code:collapse=true}table(two,batchID)
    batchID
two  0689 0848 0979 1096 1198 1440 1551 1633 1818 1871 1947 2043
  18    0    0   12    2    0    2    0    2    0    0    0    0
  21   13    0    0    0    0    0    0    4    0    0    0    0
  22    9    0    0    0    6    3    0   12    2    0    2    0
  33    0    0    0    0    4    5    0    0    1    0    1    0
  34    0    6    0    0    0    2    0    1    7    1    1    0
  37    0    0    2    6    1    0    0    1    0    0    0    0
  39    0    0    0    0    0   12    0    0    4    0    0    0
  43    0    3    2    0    0    0    2    1    4    0    1    0
  46    0    0    5    0    0    0    0    0    2    0    0    0
  51    0    0    0    3    0    0    0    0    0    0    0    1
  56    1    0    0    0    0    0    0    2    2    0    0    6
  60    0   20    0    0    1    0    0    0    1    2    0    2
  63    0    0    0    0    0    2    0    0    1    0    4    0
  66    0   18   15    0    6    0    0    0    0    0    0    0
  70    0    0    0    0    0    0    0    0    2    0    0    0
  77    0    0    0    0    0    0    0    0    0    0    4   10
  79    0    0    0    0    0    0    0    0    0    0    1    0
  85    0    0    0    0    0    0    0    0    3    0    1    0
  90    0    0    0    0    0    0    0    0    0    0    1    0
  92    0    0    0    0    0    0    0    0    0    0    0    2
  94    0    0    0    0    0    0    0    0    0    0    1    0
  96    0    0    0    0    0    0    0    0    0    0    0    2
  98    0    0    0    0    0    0    0    0    0    0    0    1{code}
Significant batch/clinical traits correlations (complete list can be found [here|^BatchClinicalInfoCorrelationsLUSC.txt]):
{csv}LUSC,DataType,NumberOfNAs,Test,Pvalue
tumor_stage,factor,27,Pearson's Chi-squared test,8.78E-14
year_of_initial_pathologic_diagnosis,integer,23,Kruskal-Wallis rank sum test,7.95E-12
days_to_form_completion,integer,30,Kruskal-Wallis rank sum test,1.48E-09
primary_tumor_pathologic_spread,factor,23,Pearson's Chi-squared test,1.96E-09
distant_metastasis_pathologic_spread,factor,29,Pearson's Chi-squared test,3.77E-05
days_to_last_followup,integer,42,Kruskal-Wallis rank sum test,7.68E-05
vital_status,factor,23,Pearson's Chi-squared test,2.37E-03
year_of_tobacco_smoking_onset,integer,116,Kruskal-Wallis rank sum test,3.12E-03
year_of_tobacco_smoking_cessation,integer,88,Kruskal-Wallis rank sum test,5.84E-03
days_to_last_known_alive,integer,75,Kruskal-Wallis rank sum test,7.37E-03
residual_tumor,factor,46,Pearson's Chi-squared test,2.00E-02
lymphnode_pathologic_spread,factor,23,Pearson's Chi-squared test,5.48E-02
age_at_initial_pathologic_diagnosis,integer,30,Kruskal-Wallis rank sum test,9.24E-02
days_to_birth,integer,30,Kruskal-Wallis rank sum test,9.73E-02{csv}

h5. Batch vs survival

Again, for this type of cancer clinical traits file contains days to last known alive but it has more NAs than days to the last follow up so I will use the latter for construction of the survival object. 


h5. DNA methylation