Batch vs center:
{code:collapse=true}> 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{code}
Significant batch/trait correlations (complete table can be found here):
{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{csv} |
