Test statistics null distributions in multiple testing : simulation studies and applications to genomics
Journal de la Société française de statistique, Volume 146 (2005) no. 1-2, pp. 77-115.
@article{JSFS_2005__146_1-2_77_0,
     author = {Pollard, Katherine S. and Birkner, Merrill D. and Van Der Laan, Mark J. and Dudoit, Sandrine},
     title = {Test statistics null distributions in multiple testing : simulation studies and applications to genomics},
     journal = {Journal de la Soci\'et\'e fran\c{c}aise de statistique},
     pages = {77--115},
     publisher = {Soci\'et\'e fran\c{c}aise de statistique},
     volume = {146},
     number = {1-2},
     year = {2005},
     language = {en},
     url = {http://www.numdam.org/item/JSFS_2005__146_1-2_77_0/}
}
TY  - JOUR
AU  - Pollard, Katherine S.
AU  - Birkner, Merrill D.
AU  - Van Der Laan, Mark J.
AU  - Dudoit, Sandrine
TI  - Test statistics null distributions in multiple testing : simulation studies and applications to genomics
JO  - Journal de la Société française de statistique
PY  - 2005
DA  - 2005///
SP  - 77
EP  - 115
VL  - 146
IS  - 1-2
PB  - Société française de statistique
UR  - http://www.numdam.org/item/JSFS_2005__146_1-2_77_0/
LA  - en
ID  - JSFS_2005__146_1-2_77_0
ER  - 
%0 Journal Article
%A Pollard, Katherine S.
%A Birkner, Merrill D.
%A Van Der Laan, Mark J.
%A Dudoit, Sandrine
%T Test statistics null distributions in multiple testing : simulation studies and applications to genomics
%J Journal de la Société française de statistique
%D 2005
%P 77-115
%V 146
%N 1-2
%I Société française de statistique
%G en
%F JSFS_2005__146_1-2_77_0
Pollard, Katherine S.; Birkner, Merrill D.; Van Der Laan, Mark J.; Dudoit, Sandrine. Test statistics null distributions in multiple testing : simulation studies and applications to genomics. Journal de la Société française de statistique, Volume 146 (2005) no. 1-2, pp. 77-115. http://www.numdam.org/item/JSFS_2005__146_1-2_77_0/

Birkner M.D., Courtine M., Dudoit S., Van Der Laan M . J., Clément K., Zucker J.D. ( 2005a). Statistical methods for detecting genotype/phenotype associations in the ObeLinks Project, Technical report, Division of Biostatistics, University of California, Berkeley, (In preparation).

Birkner M.D., Pollard K.S., Van Der Laan M.J., Dudoit S. ( 2005b). Multiple testing procedures and applications to genomics, Technical Report 168, Division of Biostatistics, University of California, Berkeley, URL www.bepress.com/ucbbiostat/paper168.

Birkner M.D., Sinisi S.E., Van Der Laan M.J. ( 2005c). Multiple testing and data adaptive regression: An application to HIV-1 séquence data, Statistical Applications in Genetics and Molecular Biology, 4(1):Article 8, URL www.bepress.com/sagmb/vol4/iss1/art8. | MR | Zbl

Calin G.A., Sevignani C., Dumitru C.D., Hyslop T., Noch E., Yendamuri S., Shimizu M., Rattan S., Bullrich F., Negrini M., Croce C.M. (2004). Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers, Proc. Natl. Acad. Sci., 101(9), p. 2999-3004.

Cheng A.M., Byrom M.W., Shelton J., Ford L.P. (2005). Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis, Nucleic Acids Research, 33(4), p. 1290-1297.

Dudoit S., Van Der Laan M.J. (2005). Multiple Testing Procedures and Applications to Genomics, Springer, (In preparation). | Zbl

Dudoit S., Shaffer J.P., Boldrick J. C. (2003). Multiple hypothesis testing in microarray experiments, Statistical Science, 18(1), p. 71-103. | MR | Zbl

Dudoit S., Van Der Laan M.J., Birkner M.D. ( 2004a). Multiple testing procedures for controlling tail probability error rates, Technical Report 166, Division of Biostatistics, University of California, Berkeley, URL www.bepress.com/ucbbiostat/paper166. | Zbl

Dudoit S., Van Der Laan M.J., Pollard K.S. ( 2004b). Multiple testing. Part I. Single-step procédures for control of general Type I error rates, Statistical Applications in Genetics and Molecular Biology, 3(1):Article 13, URL www.bepress.com/sagmb/vol3/iss1/artl3. | MR | Zbl

Hochberg Y., Tamhane A. C. (1987). Multiple Comparison Procedures, Wiley-Interscience. | MR | Zbl

Keles S., Van Der Laan M.J., Dudoit S., Cawley S.E. (2004). Multiple testing methods for ChIP-Chip high density oligonucleotide array data, Technical

Report 147, Division of Biostatistics, University of California, Berkeley, URL www. bepress. com/ucbbiostat/paper 147.

Korn E.L., Troendle J.F., Mcshane L.M., Simon R. (2004). Controlling the number of false discoveries: Application to high-dimensional genomic data, Journal of Statistical Planning and Inference, 124(2), p. 379-398. | MR | Zbl

Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Makr H., Ferrando A.A., Downing J.R., Jacks T., Horvitz H.R., Golub T.R. (2005). MicroRNA expression profiles classify human cancers, Nature, 435(9), p. 834-838, URL www.broad.mit.edu/cancer/pub/miGCM.

Michael M.Z., O'Connor S.M., Van Holst Pellekaan N. G., Young G.P., James R.J. (2003). Reduced accumulation of specifie microRNAs in colorectal neoplasia, Molecular Cancer Research, 1(12), p. 882-891.

O'Donnell K.A., Wentzel E.A., Zeller K.I., Dang C.V., Mendell J.T. (2005). c-Myc-regulated microRNAs modulate E2F1 expression, Nature, 435(7043), p. 839-843.

Pollard K.S.,Van Der Laan M.J. (2004). Choice of a null distribution in resampling-based multiple testing, Journal of Statistical Planning and Inference, 125(1-2), p. 85-100. | MR | Zbl

Pollard K.S., Van Der Laan M.J. (2005). Bioinformatics and Computational Biology Solutions Using R and Bioconductor, chapter 13: Cluster Analysis of Genomic Data, p. 209-228, Statistics for Biology and Health, Springer-Verlag, New York, URL www.bepress.com/ucbbiostat/paper167.

Pollard K.S., Dudoit S., Van Der Laan M.J. (2005). Bioinformatics and Computational Biology Solutions Using R and Bioconductor, chapter 15: Multiple Testing Procedures: The multtest Package and Applications to Genomics, p. 249-271, Statistics for Biology and Health, Springer-Verlag, New York, URL www.bepress.com/ucbbiostat/paper164.

Troendle J.F. (1995). A stepwise resampling method of multiple hypothesis testing, Journal of the American Statistical Association, 90(429), p. 370-378. | MR | Zbl

Troendle J.F. (1996). A permutational step-up method of testing multiple out-comes, Biometrics, 52(3), p. 846-859. | MR | Zbl

Van Der Laan M.J., Pollard K.S. (2003). A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap, Journal of Statistical Planning and Inference, 117(2), p. 275-303. | MR | Zbl

Van Der Laan M.J., Dudoit S., Pollard K.S. ( 2004a). Multiple testing. Part II. Step-down procédures for control of the family-wise error rate, Statistical Applications in Genetics and Molecular Biology, 3(l):Article 14, URL www.bepress.com/sagmb/vol3/issl/art14. | MR | Zbl

Van Der Laan M. J., Dudoit S., Pollard K.S. ( 2004b). Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives, Statistical Applications in Genetics and Molecular Biology, 3(1):Article 15, URL www.bepress.com/sagmb/vol3/iss1/art15. | MR | Zbl

Van Der Laan M.J., Birkner M.D., Hubbard A.E. (2005). Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives, Statistical Application in Genetics and Molecular Biology, 41(1): Article 29, URL www.bepress.com/sagmb/vol4/iss1/art29. | MR | Zbl

Westfall P.H., Young S.S. (1993). Resampling-Based Multiple Testing: Examples and Methods for p-value Adjustment, John Wiley & Sons. | Zbl

Wienholds E., Plasterk R.H.A. (2005). MicroRNA function in animal development, Federation of European Biochemical Societies Letters, 579(26), p. 5911-5922.