Comparing imputation procedures for affymetrix gene expression datasets using MAQC datasets

Advances in Bioinformatics

Volumn 2013, Issue , 2013, Pages

  Rao, Sreevidya Sadananda Sadasiva ^a   Shepherd, Lori A ^a   Bruno, Andrew E ^b   Liu, Song ^a   Miecznikowski, Jeffrey C ^a,b  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84886681634     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2013/790567     Document Type: Article

References (43)

1. Troyanskaya O., Cantor M., Sherlock G., Brown P., Hastie T., Tibshirani R., Botstein D., Altman R. B., Missing value estimation methods for DNA microarrays. Bioinformatics 2001 17 6 520 525 2-s2.0-0034960264 (Pubitemid 32600498)
2. Wold H., Path models with latent variables: the NIPALS approach. Quantitative Sociology: International Perspectives on Mathematical and Statistical Modeling 1975 307 357
3. Oba S., Sato M., Takemasa I., Monden M., Matsubara K., Ishii S., A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 2003 19 16 2088 2096 2-s2.0-0242643743 10.1093/bioinformatics/ btg287 (Pubitemid 37408160)
4. Bø T. H., Dysvik B., Jonassen I., LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research 2004 32 3 e34 2-s2.0-2342646842
5. Kim H., Golub G. H., Park H., Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 2005 21 2 187 198 2-s2.0-13444304426 10.1093/bioinformatics/bth499 (Pubitemid 40202020)
6. Ouyang M., Welsh W. J., Georgopoulos P., Gaussian mixture clustering and imputation of microarray data. Bioinformatics 2004 20 6 917 923 2-s2.0-2342426727 10.1093/bioinformatics/bth007 (Pubitemid 38559733)
7. Miecznikowski J. C., Damodaran S., Sellers K. F., Coling D. E., Salvi R., Rabin R. A., A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data. Proteome Science 2011 9 14 2-s2.0-79953082846 10.1186/1477-5956-9-14
8. Brock G. N., Shaffer J. R., Blakesley R. E., Lotz M. J., Tseng G. C., Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. BMC Bioinformatics 2008 9 1 12 2-s2.0-39749093807 10.1186/1471-2105-9-12 (Pubitemid 351298552)
9. Celton M., Malpertuy A., Lelandais G., de Brevern A. G., Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genomics 2010 11 1 15 2-s2.0-77249129377 10.1186/1471-2164-11-15
10. Oh S., Kang D. D., Brock G. N., Tseng G. C., Biological impact of missing-value imputation on downstream analyses of gene expression profiles. Bioinformatics 2011 27 1 78 86 2-s2.0-78650554266 10.1093/bioinformatics/btq613 btq613
11. Mei R., Di X., Ryder T. B., Hubbell E., Dee S., Webster T. A., Harrington C. A., Ho M.-H., Baid J., Smeekens S. P., Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 2002 18 12 1593 1599 2-s2.0-12244313858 10.1093/bioinformatics/18.12.1593 (Pubitemid 36097724)
12. Gentleman R., Carey V., Huber W., Irizarry R., Dudoit S., Bioinformatics and computational biology solutions using R and Bioconductor. Statistics for Biology and Health 2005
13. Gautier L., Cope L., Bolstad B. M., Irizarry R. A., Affy-Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004 20 3 307 315 2-s2.0-1342288026 10.1093/bioinformatics/btg405 (Pubitemid 38262761)
14. Shi L., The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 2006 24 9 1151 1161 2-s2.0-33748491517 10.1038/nbt1239 (Pubitemid 44359727)
15. Chen J. J., Hsueh H., Delongchamp R. R., Lin C., Tsai C., Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 2007 8 1 412 2-s2.0-38349088960 10.1186/1471-2105-8-412
16. Shi L., Jones W. D., Jensen R. V., Harris S. C., Perkins R. G., Goodsaid F. M., Guo L., Croner L. J., Boysen C., Fang H., Qian F., Amur S., Bao W., Barbacioru C. C., Bertholet V., Cao X. M., Chu T., Collins P. J., Fan X., Frueh F. W., Fuscoe J. C., Guo X., Han J., Herman D., Hong H., Kawasaki E. S., Li Q., Luo Y., Ma Y., Mei N., Peterson R. L., Puri R. K., Shippy R., Su Z., Sun Y. A., Sun H., Thorn B., Turpaz Y., Wang C., Wang S. J., Warrington J. A., Willey J. C., Wu J., Xie Q., Zhang L., Zhang L., Zhong S., Wolfinger R. D., Tong W., The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008 9 supplement 9 S10 2-s2.0-49649083648 10.1186/1471-2105-9-S9-S10
17. Choe S. E., Boutros M., Michelson A. M., Church G. M., Halfon M. S., Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biology 2005 6 2 R16 2-s2.0-22144461265
18. Zhu Q., Miecznikowski J. C., Halfon M. S., Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics 2010 11 1 285 2-s2.0-77952721219 10.1186/1471-2105-11-285
19. Zhu Q., Miecznikowski J. C., Halfon M. S., A wholly defined Agilent microarray spike-in dataset. Bioinformatics 2011 27 9 1284 1289 2-s2.0-79954529468 10.1093/bioinformatics/btr135 btr135
20. Affymetrix I., Statistical algorithms description document. Technical Paper 2002
21. Wilson C. L., Miller C. J., Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics 2005 21 18 3683 3685 2-s2.0-24644512209 10.1093/bioinformatics/bti605 (Pubitemid 41264111)
22. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A. J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J. Y. H., Zhang J., Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004 5 10 R80 2-s2.0-28744458859
23. Hastie T., Tibshirani R., Narasimhan B., Chu G., Impute: Imputation for Microarray Data 1999. R package version 1.10.0
24. BBø T.H., Dysvik B., Jonassen I., Lsimpute: Accurate estimation of missing values in microarray data with least squares methods. 2005, http://www.ii.uib.no/ trondb/imputation/
25. Nguyen D. V., Wang N., Carroll R. J., Evaluation of missing value estimation for microarray data. Journal of Data Science 2004 2 4 347 370
26. Stacklies W., Redestig H., PcaMethods: A Collection of PCA Methods 2007. R package version 1.18.0
27. Sadasiva Rao S. S., Shepherd L. A., Bruno A. E., Liu S., Miecznikowski J. C., A full analysis of imputation procedures for Affymetrix gene expression datasets. Technical Report 2012 1202 Buffalo, NY, USA SUNY University at Buffalo-Department of Biostatistics
28. Patterson T. A., Lobenhofer E. K., Fulmer-Smentek S. B., Collins P. J., Chu T., Bao W., Fang H., Kawasaki E. S., Hager J., Tikhonova I. R., Walker S. J., Zhang L., Hurban P., De Longueville F., Fuscoe J. C., Tong W., Shi L., Wolfinger R. D., Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nature Biotechnology 2006 24 9 1140 1150 2-s2.0-33748491718 10.1038/nbt1242 (Pubitemid 44359726)
29. Wen Z., Wang C., Shi Q., Huang Y., Su Z., Hong H., Tong W., Shi L., Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinformatics 2010 11 supplement 6 S10 2-s2.0-77957723086 10.1186/1471-2105-11-10
30. Luo J., Schumacher M., Scherer A., Sanoudou D., Megherbi D., Davison T., Shi T., Tong W., Shi L., Hong H., Zhao C., Elloumi F., Shi W., Thomas R., Lin S., Tillinghast G., Liu G., Zhou Y., Herman D., Li Y., Deng Y., Fang H., Bushel P., Woods M., Zhang J., A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics Journal 2010 10 4 278 291 2-s2.0-77955131271 10.1038/tpj.2010.57
31. Kadota K., Shimizu K., Evaluating methods for ranking differentially expressed genes applied to microArray quality control data. BMC Bioinformatics 2011 12 1 227 2-s2.0-79957927402 10.1186/1471-2105-12-227
32. Aittokallio T., Dealing with missing values in large-scale studies: microarray data imputation and beyond. Briefings in Bioinformatics 2009 11 2 253 264 2-s2.0-77950949307 10.1093/bib/bbp059 bbp059
33. Tuikkala J., Elo L. L., Nevalainen O. S., Aittokallio T., Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics 2008 9 1 202 2-s2.0-43849094303 10.1186/1471-2105-9-202 (Pubitemid 351696446)
34. Liew A., Law N., Yan H., Missing value imputation for gene expression data: computational techniques to recover missing data from available information. Briefings in Bioinformatics 2011 12 5 498 513 2-s2.0-80053185923 10.1093/bib/bbq080 bbq080
35. Bolstad B. M., Irizarry R. A., Åstrand M., Speed T. P., A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003 19 2 185 193 2-s2.0-0037316303 10.1093/bioinformatics/19.2.185 (Pubitemid 36181903)
36. Irizarry R. A., Bolstad B. M., Collin F., Cope L. M., Hobbs B., Speed T. P., Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 2003 31 4 e15 2-s2.0-12344280017
37. Irizarry R. A., Hobbs B., Collin F., Beazer-Barclay Y. D., Antonellis K. J., Scherf U., Speed T. P., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003 4 2 249 264 2-s2.0-0142121516
38. Wu Z., Irizarry R. A., Gentleman R., Martinez-Murillo F., Spencer F., A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 2004 99 468 909 917 2-s2.0-10844290766 10.1198/016214504000000683 (Pubitemid 39665934)
39. Dabney A. R., Storey J. D., A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biology 2006 7 3 401 2-s2.0-33745023798 10.1186/gb-2006-7-3-401 (Pubitemid 43871867)
40. Gaile D. P., Miecznikowski J. C., Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent. BMC Genomics 2007 8 1 105 2-s2.0-34250741568 10.1186/1471-2164-8-105 (Pubitemid 46951222)
41. Perkel J. M., Six things you won't find in the MAQC. The Scientist 2007 20 11 68
42. Liang P., MAQC papers over the cracks. Nature Biotechnology 2007 25 1 27 28 2-s2.0-33846122647 10.1038/nbt0107-27 (Pubitemid 46087889)
43. Shi L., Jones W. D., Jensen R. V., Wolfinger R. D., Kawasaki E. S., Herman D., Guo L., Goodsaid F. M., Tong W., Reply to MAQC papers over the cracks. Nature Biotechnology 2007 25 28 29