twilight.teststat          package:twilight          R Documentation

_I_n_t_e_r_f_a_c_e _t_o _t_h_e _t_e_s_t _s_t_a_t_i_s_t_i_c_s _p_r_o_v_i_d_e_d _w_i_t_h_i_n '_t_w_i_l_i_g_h_t'

_D_e_s_c_r_i_p_t_i_o_n:

     A function to compute two-sample t, Z and fold change equivalent
     test statistics (paired or unpaired) and correlation coefficients.

_U_s_a_g_e:

     twilight.teststat(xin, yin, method = "fc", paired = FALSE, s0 = NULL)

_A_r_g_u_m_e_n_t_s:

     xin: Either an expression set ('ExpressionSet') or a data matrix
          with rows corresponding to features and columns corresponding
          to samples. 

     yin: A numerical vector containing class labels. The higher label
          denotes the case, the lower label the control samples to test
          case vs. control. For correlation scores, 'yin' can be any
          numerical vector of length equal to the number of samples. 

  method: Character string: '"fc"' for fold change equivalent test
          (that is log ratio test), '"t"' for t-test, and '"z"' for
          Z-test of Tusher et al. (2001). With '"pearson"' or
          '"spearman"', the test statistic is either Pearson's
          correlation coefficient or Spearman's rank correlation
          coefficient.

  paired: Logical value. Depends on whether the samples are paired.
          Ignored if 'method="pearson"' or 'method="spearman"'.

      s0: Fudge factor for variance correction in the Z-test. Takes
          effect only if 'method="z"'. If 's0=NULL': The fudge factor
          is set to the median of the pooled standard deviations.

_D_e_t_a_i_l_s:

     Please see vignette for detailed information.

_V_a_l_u_e:

     Returns a list with two components: a numerical vector of observed
     test statistics 'observed'. Each entry corresponds to one row of
     the input data matrix. Also, the estimated fudge factor 's0' is
     returned. In any other case except 'method="z"', 's0' is zero.

_A_u_t_h_o_r(_s):

     Stefanie Scheid <URL: http://www.molgen.mpg.de/~scheid>

_R_e_f_e_r_e_n_c_e_s:

     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.

_S_e_e _A_l_s_o:

     'twilight.pval'

_E_x_a_m_p_l_e_s:

     ### Z-test on random values
     M <- matrix(rnorm(20000),nrow=1000)
     id <- c(rep(1,10),rep(0,10))
     stat <- twilight.teststat(M,id,method="z")

     ### Pearson correlation
     id <- 1:20
     stat <- twilight.teststat(M,id,method="pearson")

