HVDMcheck               package:rHVDM               R Documentation

_C_h_e_c_k_s _t_h_a_t _a_n _o_b_j_e_c_t _o_f _c_l_a_s_s _E_x_p_r_e_s_s_i_o_n_S_e_t _i_s _c_o_m_p_l_i_a_n_t _w_i_t_h _H_V_D_M

_D_e_s_c_r_i_p_t_i_o_n:

     This method issues warnings about the compliance of the
     ExpressionSet object to be used with rHVDM. It just issues
     warnings and does not attempt to correct the problems encountered.
     the 'pdata' argument is optional; if missing, the method will
     check the phenodata that is inside the ExpressionSet.

_U_s_a_g_e:

     HVDMcheck(eset,pdata)

_A_r_g_u_m_e_n_t_s:

    eset: an ExpressionSet object (Biobase) 

   pdata: a dataframe (optional argument) 

_D_e_t_a_i_l_s:

     The checks performed are: A) the phenoData has all the required
     fields. B) the time field is numeric, has a zero time point, does
     not have negative or repeated values. C) the row names in the
     phenoData  are consistent with the columns names found in the
     exprSet. D) the data is not log-transformed. E) Standard
     deviations have been supplied in the ExpressionSet, and they are
     non-negative.

_V_a_l_u_e:

     no value returned.

_N_o_t_e:

     If the 'pdata' argument is ignored (it can be),  the method checks
     the phenoData that is inside the ExpressionSet.

_A_u_t_h_o_r(_s):

     Martino Barenco

_R_e_f_e_r_e_n_c_e_s:

     M. Barenco, D. Tomescu, D. Brewer, R. Callard, J. Stark, M. Hubank
     (2006) Ranked predictions of p53 targets using Hidden Variable
     Dynamic Modelling. _Genome Biology_, *V7(3)*, R25.

_S_e_e _A_l_s_o:

     'training'

_E_x_a_m_p_l_e_s:

     data(HVDMexample)
     HVDMcheck(fiveGyMAS5)

