Page Comparison

h5. Batch vs clinical traits

Batch vs center:
{code}> table(batchID,center)
       center
batchID B7 BR CD CG D7 EQ F1
   1129  0 31  0  0  0  0  0
   1156  0 12  0 23  0  0  0
   1601  2  0  7 16  3  1  0
   1801  0  9  0  3 10  0  1
   1883  0 11  0  0  5  0  1{code}
Most significant correlations (complete list can be found [here|^BatchClinicalInfoCorrelationsSTAD.txt])
{csv}STAD,DataType,NumberOfNAs,Test,Pvalue
residual_tumor,factor,8,Pearson's Chi-squared test,8.06E-17
year_of_initial_pathologic_diagnosis,integer,1,Kruskal-Wallis rank sum test,2.88E-13
days_to_form_completion,integer,1,Kruskal-Wallis rank sum test,3.72E-11
days_to_last_followup,integer,1,Kruskal-Wallis rank sum test,5.15E-11
primary_tumor_pathologic_spread,factor,1,Pearson's Chi-squared test,1.68E-06
histological_type,factor,6,Pearson's Chi-squared test,5.82E-06
lymphnode_pathologic_spread,factor,1,Pearson's Chi-squared test,6.09E-05
number_of_lymphnodes_examined,integer,53,Kruskal-Wallis rank sum test,1.25E-04
vital_status,factor,1,Pearson's Chi-squared test,2.95E-03
tumor_stage,factor,31,Pearson's Chi-squared test,3.49E-02{csv}
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h5. Batch vs survival 
!KaplanMeierCurveSTAD.png|thumbnail! !SurvivalByBatchSTAD.png|thumbnail!
{code:collapse=true}Call:
coxph(formula = survivalObject ~ batchVector)

  n= 134, number of events= 14

                     coef exp(coef)  se(coef)     z Pr(>|z|)
batchVector1156 1.722e+01 3.012e+07 7.152e+03 0.002    0.998
batchVector1601 1.786e+01 5.728e+07 7.152e+03 0.002    0.998
batchVector1801 1.663e+01 1.665e+07 7.152e+03 0.002    0.998
batchVector1883        NA        NA 0.000e+00    NA       NA

                exp(coef) exp(-coef) lower .95 upper .95
batchVector1156  30117568  3.320e-08         0       Inf
batchVector1601  57279474  1.746e-08         0       Inf
batchVector1801  16645384  6.008e-08         0       Inf
batchVector1883        NA         NA        NA        NA

Rsquare= 0.026   (max possible= 0.496 )
Likelihood ratio test= 3.58  on 3 df,   p=0.3109
Wald test            = 2.13  on 3 df,   p=0.545
Score (logrank) test = 3.1  on 3 df,   p=0.3762
Warning messages:
1: In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Loglik converged before variable  1,2,3 ; beta may be infinite.
2: In coxph(survivalObject ~ batchVector) :
  X matrix deemed to be singular; variable 4{code}
No correlation with survival. For some reason I got NAs and an error for the last batch although it is definitely not because of the unused factor levels. 
h5. DNA methylation