plateEffects            package:cellHTS2            R Documentation

_A_c_c_e_s_s _p_l_a_t_e _e_f_f_e_c_t_s _s_t_o_r_e_d _i_n _a _c_e_l_l_H_T_S _o_b_j_e_c_t.

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

     This generic function accesses plate effects stored in slot
     'rowcol.effects' and 'overall.effects'  of a 'cellHTS' instance.

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

     plateEffects(object)

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

  object: Object derived from class 'cellHTS' that has been normalized
          by a spatial normalization method. See details.

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

     'plateEffects' returns a list with two elements: 'rowcol' and
     'overall'.

     'plateEffects[["rowcol"]]' corresponds to the contents of slot
     'rowcol.effects' of 'object'. This is a 3D array with the same
     dimensions as 'Data(object)': 'nr of Features x nr of Samples x nr
     of Channels' of the current 'cellHTS' object.

     'plateEffects[["overall"]]' contains the data stored in slot
     'overall.effects' of 'object'. This is a 3D array with dimensions
     'nr Plates x nr Samples x nr Channels' of 'object'. Slot
     'overall.effects' is only estimated when B score method is used to
     normalize the data. 

     Note that these 2 slots accessed by this function were stored
     after preprocessing the data either using Bscore method or local
     regression fit (see 'normalizePlates' for details), by setting the
     option 'save.model=TRUE'.

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

     Ligia Bras ligia@ebi.ac.uk

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

     'cellHTS' 'normalizePlates' 'Bscore' 'spatialNormalization'

