RankingFoxDimmic        package:GeneSelector        R Documentation

_R_a_n_k_i_n_g _b_a_s_e_d _o_n _t_h_e _t-_s_t_a_t_i_s_t_i_c _o_f _F_o_x _a_n_d _D_i_m_m_i_c

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

     Performs a two-sample bayesian t test on a gene expression matrix
     using the methodology by Fox and Dimmic (2006).
      For 'S4' method information, see RankingFoxDimmic-methods.

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

     RankingFoxDimmic(x, y, type = "unpaired", m = 8, pvalues = TRUE, 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'.

       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'.


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

          '"paired"' and '"unpaired"' are not possible for this kind of
          test.

       m: The number of similarly expressed genes to use for
          calculating Bayesian variance and prior degrees of freedom.
          The default value suggested by Fox and Dimmic is currently 8,
          s. note.

 pvalues: Should p-values be computed ? Default is 'TRUE'.

gene.names: An optional vector of gene names.

     ...: Currently unused argument.

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

     An object of class GeneRanking.

_N_o_t_e:

     Although the test of Fox and Dimmic is very similar to the one
     proposed by Baldi and Long, there are various slight differences,
     in particular with respect to the computation of the bayesian
     variance.

_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:

     Fox, R.J., Dimmic, M.W. (2006). 
      A two sample Bayesian t-test for microarray data. _BMC
     Bioinformatics, 7:126_

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

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

