expval               package:twilight               R Documentation

_E_x_a_m_p_l_e _o_f _t_w_i_l_i_g_h_t._p_v_a_l _r_e_s_u_l_t

_D_e_s_c_r_i_p_t_i_o_n:

     Application of function 'twilight.pval' on leukemia data set of
     Golub et al. (1999), as given in 'data(Golub_Merge)' in
     'library(golubEsets)'.

     First step was the variance-stabilizing normalization of Huber et
     al. (2002) in 'library(vsn)': 'golubNorm <- justvsn(Golub_Merge)'.

     The function call was then 'expval <- twilight.pval(golubNorm,id)'
     with 'id <- as.numeric(Golub_Merge$ALL.AML)'.

_U_s_a_g_e:

     data(expval)

_F_o_r_m_a_t:

     A twilight object.

_R_e_f_e_r_e_n_c_e_s:

     Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP,
     Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD and
     Lander ES (1999): Molecular Classification of Cancer: Class
     Discovery and Class Prediction by Gene Expression Monitoring,
     _Science_ *286*, 531-537.

     Huber W, von Heydebreck A, Sultmann H, Poustka A and Vingron M
     (2002): Variance stabilization applied to microarray data
     calibration and to the quantification of differential expression,
     _Bioinformatics_ *18*, suppl. 1, S96-S104.

     Scheid S and Spang R (2004): A stochastic downhill search
     algorithm for estimating the local false discovery rate, _IEEE
     TCBB_ *1(3)*, 98-108.

     Scheid S and Spang R (2005): twilight; a Bioconductor package for
     estimating the local false discovery rate, _Bioinformatics_
     *21(12)*, 2921-2922. 

     Scheid S and Spang R (2006): Permutation filtering: A novel
     concept for significance analysis of large-scale genomic data, in:
     Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M
     (Eds.): _Research in Computational Molecular Biology: 10th Annual
     International Conference, Proceedings of RECOMB 2006, Venice,
     Italy, April 2-5, 2006_. Lecture Notes in Computer Science vol.
     3909, Springer, Heidelberg, pp. 338-347.

     Tusher VG, Tibshirani R and Chu G (2001): Significance analysis of
     mircroarrays applied to the ionizing response, _PNAS_ *98(9)*,
     5116-5121.

