xde                   package:XDE                   R Documentation

_F_i_t _t_h_e _B_a_y_e_s_i_a_n _h_i_e_r_a_r_c_h_i_c_a_l _m_o_d_e_l _f_o_r _c_r_o_s_s-_s_t_u_d_y _d_i_f_f_e_r_e_n_t_i_a_l
_g_e_n_e _e_x_p_r_e_s_s_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Fits the Bayesian hierarchical model for cross-study differential
     gene expression.

_U_s_a_g_e:

       
       xde(paramsMcmc, esetList, outputMcmc)

_A_r_g_u_m_e_n_t_s:

paramsMcmc: Object of class 'XdeParameter'

esetList: Object of class 'ExpressionSetList'

outputMcmc: Object of class 'XdeMcmc' (optional)

_D_e_t_a_i_l_s:

     Details for fitting the Bayesian model are discussed elsewhere
     (see citation below and XdeParameterClass vignette)

_V_a_l_u_e:

     Object of class 'XdeMcmc'

_N_o_t_e:

     See the vignettes for XdeParameterClass and XDE.

_A_u_t_h_o_r(_s):

     R. Scharpf

_R_e_f_e_r_e_n_c_e_s:

     R. Scharpf et al., A Bayesian Model for Cross-Study Differential
     Gene Expression, Technical Report 158, Johns Hopkins University,
     Department of Biostatistics, 2007

_S_e_e _A_l_s_o:

     'XdeMcmc-class', 'XdeParameter-class', 'ExpressionSetList-class'

_E_x_a_m_p_l_e_s:

     ## Not run: 
       data(expressionSetList)
       xparam <- new("XdeParameter", phenotypeLabel="adenoVsquamous", esetList=expressionSetList)
       iterations(xparam) <- 10
       fit <- xde(xparam, esetList=expressionSetList)
     ## End(Not run)

