KIRC kidney renal cell carcinoma

Batch vs clinical traits

Clinical traits: 36, number of batches: 13

Batch vs center:

> table(batchID,two)
       two
batchID A3 AK AS B0 B2 B4 B8 BP CJ CW CZ DV EU
   0859 31  8  2  0  0  0  0  0  0  0  0  0  0
   1186  4  6  0  0  5  0  6  5  9  0  0  0  0
   1275  0 12  0 29  1  0  1  0  0  0  0  0  0
   1284  0  0  0  0  0  0  0 50  0  0  0  0  0
   1303  0  0  0  6  0  0  0 11 24  0  6  0  0
   1323 18  7  0  0  4  0  3  5  9  0  0  0  0
   1332  0  0  0  6  0  0  0 39  2  0  0  0  0
   1418  6  0  0 27  0  0  6  8  0  0  0  0  0
   1424  0  0  0  0  0  0  0 28 16  0  3  0  0
   1500  0  1  0 15  0  2  1  1  0  0 24  0  0
   1536  2  0  0 18  5  0  5  0 13  9  0  9  0
   1551  0  0  0  0  0  0  3  0  0  0  0  0  0
   1670  0  0  0  6  0  7  4  0  7  6  7  0  4

Significant batch/trait correlations (complete table can be found here):

Unknown macro: {csv}

KIRC_clinical_traits,DataType,NumberOfNAs,Test,Pvalue
white_cell_count_result,factor,82,Pearson's Chi-squared test,2.09E-13
serum_calcium_result,factor,160,Pearson's Chi-squared test,8.31E-13
tumor_stage,factor,21,Pearson's Chi-squared test,2.11E-11
tumor_grade,factor,5,Pearson's Chi-squared test,6.43E-09
vital_status,factor,0,Pearson's Chi-squared test,9.62E-09
days_to_form_completion,integer,0,Kruskal-Wallis rank sum test,1.16E-07
year_of_initial_pathologic_diagnosis,integer,0,Kruskal-Wallis rank sum test,1.38E-07
days_to_last_known_alive,integer,10,Kruskal-Wallis rank sum test,8.41E-07
days_to_last_followup,integer,4,Kruskal-Wallis rank sum test,1.94E-06
distant_metastasis_pathologic_spread,factor,11,Pearson's Chi-squared test,2.23E-06
primary_tumor_pathologic_spread,factor,0,Pearson's Chi-squared test,3.63E-06
person_neoplasm_cancer_status,factor,28,Pearson's Chi-squared test,4.26E-06
hemoglobin_result,factor,71,Pearson's Chi-squared test,2.66E-04
lymphnode_pathologic_spread,factor,2,Pearson's Chi-squared test,7.85E-04
lymphnodes_examined_prior_presentation,factor,43,Pearson's Chi-squared test,2.05E-03
gender,factor,0,Pearson's Chi-squared test,2.10E-02
age_at_initial_pathologic_diagnosis,integer,0,Kruskal-Wallis rank sum test,2.51E-02
days_to_birth,integer,8,Kruskal-Wallis rank sum test,2.87E-02
prior_diagnosis,factor,0,Pearson's Chi-squared test,4.75E-02

Survival vs Batch

Summary can be found here, batch is significantly correlated with survival:
Likelihood ratio test= 61.35 on 10 df, p=2.007e-09
Wald test = 64.35 on 10 df, p=5.39e-10
Score (logrank) test = 75.35 on 10 df, p=4.066e-12

DNA methylation data analysis

27k dataset, downloaded on December 28, 2011. 219 samples. Technical variables available: batch, amount, concentration, day of shipment, month of shipment, year of shipment, plate row, plate column. Combine day, month and year in a single variable. Info about technical variables:

> head(methNew)
    batchID  amount concentration plate_column plate_row dateCombined
2      0859 26.7 uL    0.14 ug/uL            1         A    17-3-2010
32     0859 26.7 uL    0.17 ug/uL            1         C    17-3-2010
59     0859 26.7 uL    0.15 ug/uL            1         D    17-3-2010
84     0859 26.7 uL    0.15 ug/uL            1         E    17-3-2010
110    0859 26.7 uL    0.15 ug/uL            1         F    17-3-2010
124    0859 26.7 uL    0.15 ug/uL            1         G    17-3-2010
> table(methNew$batchID)

0859 1186 1275 1284 1303 1323 1332 1418 1424 1500 1536 1551 1670
  40   35    0   50   47    0   47    0    0    0    0    0    0
> table(methNew$amount)

10.3 uL   10 uL 11.2 uL   11 uL 12.4 uL 13.2 uL 13.3 uL 15.7 uL   15 uL 16.1 uL
      0       0       0       0       0       0       0       0       0       0
16.3 uL 16.7 uL   16 uL   17 uL   19 uL 20.9 uL   20 uL 21.5 uL   22 uL 23.7 uL
      0       0       0       0       0       0       0       0       0       0
  25 uL 26.7 uL   30 uL   40 uL    5 uL   60 uL   61 uL 63.1 uL 66.6 uL 6.67 uL
      0     219       0       0       0       0       0       0       0       0
66.7 uL  6.7 uL  7.2 uL   80 uL  8.9 uL
      0       0       0       0       0
#It seems that all values of the amount are 26.7 (although I have factor levels from the all values available for future DNA methylation datasets for patients for whom samples are already collected)
> table(methNew$concentration)

  0.01 ug/uL   0.03 ug/uL   0.04 ug/uL 0.0500 ug/uL  0.050 ug/uL   0.05 ug/uL
           0            0            0            0            0            0
  0.09 ug/uL  0.100 ug/uL   0.10 ug/uL   0.11 ug/uL   0.12 ug/uL   0.13 ug/uL
           0            0            0            0            0            7
  0.14 ug/uL   0.15 ug/uL   0.16 ug/uL   0.17 ug/uL    0.1 ug/uL   0.50 ug/uL
          50          122           30           10            0            0
   .05 ug/uL    0.5 ug/uL   .100 ug/uL   .150 ug/uL     .1 ug/uL    .50 ug/uL
           0            0            0            0            0            0
    .5 ug/uL
           0
> table(methNew$plate_column)

 1  2  3  4  5  6  7
39 40 40 40 35 23  2
> table(methNew$plate_row)

 A  B  C  D  E  F  G  H
30 28 28 27 27 27 27 25
> table(methNew$plate_row,methNew$plate_column)

    1 2 3 4 5 6 7
  A 5 5 5 5 5 4 1
  B 4 5 5 5 5 3 1
  C 5 5 5 5 5 3 0
  D 5 5 5 5 4 3 0
  E 5 5 5 5 4 3 0
  F 5 5 5 5 4 3 0
  G 5 5 5 5 4 3 0
  H 5 5 5 5 4 1 0
> table(methNew$dateCombined)

11-10-2010  17-3-2010  25-8-2010  27-9-2010  6-10-2010
        47         40         35         50         47
> table(methNew$dateCombined,methNew$batchID)

             0859 1186 1275 1284 1303 1323 1332 1418 1424 1500 1536 1551 1670
  11-10-2010    0    0    0    0    0    0   47    0    0    0    0    0    0
  17-3-2010    40    0    0    0    0    0    0    0    0    0    0    0    0
  25-8-2010     0   35    0    0    0    0    0    0    0    0    0    0    0
  27-9-2010     0    0    0   50    0    0    0    0    0    0    0    0    0
  6-10-2010     0    0    0    0   47    0    0    0    0    0    0    0    0