STAD stomach adenocarcinoma

Batch vs clinical traits

Batch vs center:

> 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

Most significant correlations (complete list can be found here)

Unknown macro: {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

Batch vs survival

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

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.

STAD stomach adenocarcinoma

Batch vs clinical traits

Batch vs survival

DNA methylation