Supplementary:

- R Programs

assoc_tests.r

- This R program provides one example of computing the statistics and

permutation p-values for one test gene,*CCNA2*, based on 8 methods

discussed in the manuscript.

- The outputs, including 8 statistics and their p-values for
*CCNA2*, will show

on the R console after the program is sucessfully excuted.

- The permutation p-value would be slightly altered due to its nature of randomness.

- To run the R code, copy all commands in the file and paste them on R console.

R is a freely available language and environment for statistical computing and

graphics. It can be downloaded from http://www.r-project.org/

- This R program provides one example of computing the statistics and
- Microarray data had been deposited to GEO database with accession number GSE9309. Only part of samples in GSE9309 were used for this study. They were GSM237139,
GSM237140,
GSM237141,
GSM237143,
GSM237144,
GSM237148,
GSM237149,
GSM237150,
GSM237151,
GSM237152,
GSM237153,
GSM237154,
GSM237155,
GSM237156,
GSM237157,
GSM237158,
GSM237159,
GSM237161,
GSM237165,
GSM237166,
GSM237167,
GSM237168,
GSM237174,
GSM237175,
GSM237176,
GSM237177,
GSM237178,
GSM237179,
GSM237180,
GSM237181,
GSM237182,
GSM237183,
GSM237184,
GSM237185,
GSM237186,
GSM237187,
GSM237188,
GSM237190,
GSM237191,
GSM237193,
GSM237194,
GSM237195,
GSM237197,
GSM237198,
GSM237199,
GSM237200,
GSM237202, and
GSM237203.

We also note that the rank-invariant linear LOWESS is the same with the rank consistent LOWESS, which is the official term applied by Agilent.