RankingBstat          package:GeneSelector          R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n _t_h_e _B-_s_t_a_t_i_s_t_i_c

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

     The B-statistic was motivated in a bayesian framework described by
     Lonnstedt and Speed (2002). It is implemented in the package
     'sma', the function is just a wrapper.
      For 'S4' method information, see RankingBstat-methods.

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

     RankingBstat(x, y, type = c("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'


          "_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.

          '"unpaired"' is _not_ possible.

gene.names: An optional vector of gene names.

     ...: Furher arguments passed to 'stat.bayesian' from the package
          'sma'

_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:

     Lonnstedt, I., Speed, T. (2002). 
      Replicated microarray data. _Statistica sinica, 12, 31-46_

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

     GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT,
     RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma,
      RankingEbam, RankingWilcEbam, RankingSam,  RankingShrinkageT,
     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 RankingBstat
     Bstat <- RankingBstat(xx, yy, type="paired")

