Supplementary

Supplementary

     We compared the results of T test on beta values with chi-square test on SMP genotypes (MM vs. MU vs. UU, 2×3 contingency table) using a case-control data set GSE49031 (including 797 pediatric acute lymphoblastic leukemia patients and 148 normal controls, total 482421 DNA methylation loci). We chose several threshold levels, such as 0.01, 0.001, 1e-5, to observe the consistency of the results identified by T test on beta values and chi-square test on SMP genotypes.
    Table 1-4 showed that the consistency is increasing with the increase of Fold Change (FC, the average beta value of one group divided by the average of the second groups) between two sample groups. All the results can be found as following:

 

Table1. fold_change>1.5

threshold levels	results of T test (n)	results of chi-square test (n)	overlap	consistency
0.05	76889	76575	76201	0.993
0.01	74322	75515	72962	0.974
0.001	70515	72665	67634	0.945
1e-4	68264	69040	63674	0.928
1e-5	66473	62301	60054	0.934

 

Table2. fold_change>2

threshold levels	results of T test (n)	results of chi-square test (n)	overlap	consistency
0.05	48963	48816	48816	0.998
0.01	48963	48625	48625	0.997
0.001	48916	47734	47723	0.988
1e-4	48550	46099	46012	0.973
1e-5	47998	43998	43870	0.956

 

Table3. fold_change>2.5

threshold levels	results of T test (n)	results of chi-square test (n)	overlap	consistency
0.05	35586	35557	35557	0.9996
0.01	35586	35521	35521	0.9991
0.001	35586	35334	35334	0.9965
1e-4	35586	34796	34796	0.9889
1e-5	35578	33730	33730	0.9740

 

Table4. fold_change>3

threshold levels	results of T test (n)	results of chi-square test (n)	overlap	consistency
0.05	26542	26540	26540	0.99996
0.01	26542	26532	26532	0.99981
0.001	26542	26505	26505	0.99930
1e-4	26542	26386	26386	0.99706
1e-5	26542	26013	26013	0.99003

 

The supplementary can also be download in doc file.

supplementary doc file:    supplementary.doc