RankingShrinkageT        package:GeneSelector        R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n _t_h_e '_s_h_r_i_n_k_a_g_e _t' _s_t_a_t_i_s_t_i_c

_D_e_s_c_r_i_p_t_i_o_n:

     The shrinkage t statistic stabilizes the estimated variances
     appearing in the denominator of the statistic via a 
     James-Stein-Shrinkage approach (Opgen-Rhein and Strimmer,2007). In
     this implementation, the shrinkage target is the median of the
     variances.
      For 'S4' method information, see RankingShrinkageT-methods.

_U_s_a_g_e:

     RankingShrinkageT(x, y, type = c("unpaired", "paired", "onesample"), gene.names = NULL, ...)

_A_r_g_u_m_e_n_t_s:

       x: A 'matrix' of gene expression values with rows corresponding
          to genes and columns corresponding to observations or
          alternatively an object of class 'ExpressionSet'.
           If 'type = paired', the first half of the columns
          corresponds to  the first measurements and the second half to
          the second ones.  For instance, if there are 10 observations,
          each measured twice, stored in an expression matrix 'expr', 
          then 'expr[,1]' is paired with 'expr[,11]', 'expr[,2]' with
          'expr[,12]', and so on.

       y: If 'x' is a matrix, then 'y' may be a 'numeric' vector or a
          factor with at most two levels.
           If 'x' is an 'ExpressionSet', then 'y' is a character
          specifying the phenotype variable in the output from 'pData'.
           If 'type = paired', take care that the coding is analogously
          to the requirement concerning 'x'


          "_u_n_p_a_i_r_e_d": two-sample test.

          "_p_a_i_r_e_d": paired test. Take care that the coding of 'y' is
               correct (s. above)

          "_o_n_e_s_a_m_p_l_e": 'y' has only one level.  Test whether the true
               mean is different from zero.


gene.names: An optional vector of gene names.

     ...: Currently unused argument.

_V_a_l_u_e:

     An object of class GeneRanking.

_A_u_t_h_o_r(_s):

     Martin Slawski martin.slawski@campus.lmu.de 
      Anne-Laure Boulesteix <URL: http://www.slcmsr.net/boulesteix>

_R_e_f_e_r_e_n_c_e_s:

     Opgen-Rhein, R., Strimmer, K. (2007). 
      Accurate Ranking of Differentially Expressed Genes  by a
     Distribution-Free Shrinkage Approach. _Statistical Applications in
     Genetics and Molecular Biology, Vol. 6, Iss. 1, Art.9_

_S_e_e _A_l_s_o:

     GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT,
     RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma,
      RankingEbam, RankingWilcEbam, RankingSam,  RankingBstat,
     RankingSoftthresholdT,  RankingPermutation, RankingGap

_E_x_a_m_p_l_e_s:

     ### Load toy gene expression data
     data(toydata)
     ### class labels
     yy <- toydata[1,]
     ### gene expression
     xx <- toydata[-1,]
     ### run RankingShrinkageT
     shrinkaget <- RankingShrinkageT(xx, yy, type="unpaired")

