empiricalStart              package:XDE              R Documentation

_E_m_p_i_r_i_c_a_l _s_t_a_r_t_i_n_g _v_a_l_u_e_s _f_o_r _t_h_e _M_C_M_C

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

     Empirical starting values for the MCMC are based on data in
     objects of class 'ExpressionSetList'

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

     empiricalStart(object, zeroNu = FALSE, phenotypeLabel, one.delta=FALSE, T_THRESH=4)

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

  object: An object of class 'ExpressionSetList'

  zeroNu: Logical: if TRUE, the nu in the Bayesian model are not
          modeled - set to zero and not updated in the MCMC.  Setting
          zeroNu to TRUE should be regarded as experimental

phenotypeLabel: character: binary phenotype.  phenotypeLabel must be in
          the varLabels of each ExpressionSet object

one.delta: delta in the Bayesian model is a gene-specific indicator for
          differential expression.  If one.delta is FALSE, we assume
          that a gene can be differentially expressed in a subset of
          studies.  When TRUE, we assume that a gene is differentially
          expressed in all studies or in none.

T_THRESH: A threshold of t-statistics (calculated row-wise for each
          study) for determining starting values of the differential
          expression indicator, delta.

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

     A list containing starting values for the MCMC that are derived
     from empirical estimates of the data.

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

     R. Scharpf

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

     'zeroNu', 'XdeParameter-class', 'ExpressionSetList-class'

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

     data(expressionSetList)
     eList <- studyCenter(expressionSetList)
     empirical <- empiricalStart(eList, phenotypeLabel="adenoVsquamous", T_THRESH=3)
     ##By default, initial values for the MCMC are sampled from the prior
     ##when initializing an object of class XdeParamater
     params <- new("XdeParameter", esetList=eList,
                   phenotypeLabel="adenoVsquamous", one.delta=FALSE, burnin=TRUE)
     ##The initial values can be replaced by empirical values as follows:
     firstMcmc(params) <- empirical

