Microarray Missing Value Imputation: Supplementary Materials
References
 Z. Cai,
M. Heydari, and
G. Lin.
Iterated Local Least Squares Imputation for Microarray Missing Values.
Journal of Bioinformatics and Computational Biology.
4(5)(2006), 935957.
 Z. Cai,
M. Heydari, and
G. Lin.
Microarray Missing Value Imputation by Iterated Local Least Squares.
In Proceedings of the Fourth AsiaPacific Bioinformatics Conference (APBC 2006).
Taipei, Taiwan. February 1316, 2006.
Pages 159168, 2006.
Release Notes
 On May 12, 2006, the following supplementary materials were released:
 On March 11, 2006, the following supplementary materials were released:
 Six microarray datasets (Alpha, Cyc.a, Cyc.b, Elu, Env, Ta.crc) in MATLAB format:
each with a complete dataset and 10 versions of randomly created missing values with 1%, 2%, 3%, 4%, 5%, 10%, 15%, and
20% missing rates (zipped, 62.1MB).
 10 NRMSE values of each of the six methods KNNimpute, SKNN, BPCA, LLSimpute, LinCmb, and ILLSimpute on the six microarray datasets
with eight different missing rates (zipped, 13KB).
 Average runtimes per run (in minutes) of each of the six methods KNNimpute, SKNN, BPCA, LLSimpute, LinCmb, and ILLSimpute on
the six microarray datasets with eight different missing rates (zipped, 2KB).
 10 NRMSE values of each of the four methods KNNimpute, INNimpute, LLSimpute, and ILLSimpute on the six microarray datasets
with eight different missing rates (zipped, 9KB).
 Average runtimes per run (in minutes) of each of the four methods KNNimpute, INNimpute, LLSimpute, and ILLSimpute on
the six microarray datasets with eight different missing rates
(zipped, 2KB).
 Average NRMSE values (over 10 runs) of ILLSimpute method on the Elu and Cyc.b datasets with 10% missing rate and 5 iterations,
using 0.51.5 ratios (468B);
Average NRMSE values (over 10 runs) of ILLSimpute method on the Elu and Cyc.b datasets with 10% missing rate and ratio 0.6,
after 110 iterations (470B).
 The (average) numbers of coherent genes selected by LLSimpute and ILLSimpute (w/5 iterations) methods on the Cyc.bdatasets with
eight different missing rates.
 1%
 2%
 3%
 4%
 5%
 10%
 15%
 20%

k in LLSimpute
NRMSE
 140
0.2856
 140
0.3346
 140
0.4234
 140
0.4496
 210
0.4595
 210
0.6459
 210
0.6736
 210
0.7076

Ratio δ in ILLSimpute
Average k
NRMSE
 0.9
139
0.2043
 0.9
139
0.1782
 1.2
181
0.2315
 0.9
139
0.2550
 1.3
190
0.2586
 0.8
119
0.5141
 1.4
197
0.5742
 1.3
190
0.6409

 MATLAB code for ILLSimpute method (8K).
Acknowledgments
This research is partially supported by CFI and NSERC.
Feedback
Please email ghlin[at]cs[dot]ualberta[dot]ca for any additional questions you might have.
