spatialNormalization        package:cellHTS2        R Documentation

_S_p_a_t_i_a_l _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Correction of spatial plate effects of data stored in slot
     'assayData' of a 'cellHTS' object by fitting a polynomial surface
     within each plate using local regression ('loess' or 'robust local
     fit'). Uses a second degree polynomial (local quadratic fit). Only
     wells containing "sample" are considered to fit the models.

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

     spatialNormalization(object, model="locfit", smoothPar=0.6,
     save.model=FALSE)

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

  object: a 'cellHTS' object that has already been configured.

   model: character indicated whether the polynomial surface should be
          fitted using robust "locfit" or "loess". The default is
          "locfit".

smoothPar: numeric. The default is 'smoothPar=0.6'. The parameter which
          controls the degree of smoothing (corresponds to 'span'
          argument of 'loess', or to the parameter 'nn' of 'lp' of
          locfit).

save.model: a logical value specifying whether the per-plate spatial
          effects should be stored in slot 'rowcol.effects' of
          'object'. See details.

_D_e_t_a_i_l_s:

     For convenience, this function should be called indireclty from
     'normalizePlates' function.

     The normalization is performed separately for each replicate and
     channel, in a per-plate fashion using the chosen local regression
     model. The polynomical surfaces are fitted using the wells
     containing "sample".

     If 'save.model=TRUE', the models row and column offsets are stored
     in the slot 'rowcol.effects' of 'object'.

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

     An object of class 'cellHTS' with normalized data stored in slot
     'assayData'.  Furthermore, if 'save.model=TRUE', the row and
     column estimated offsets are stored in the slot 'rowcol.effects'. 
     This slot is a 3D array with the same dimension as 'Data(object)'.

     Moreover, the processing status of the 'cellHTS' object is updated
     in the slot 'state' to 'object@state[["normalized"]]=TRUE'.

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

     Ligia Bras ligia@ebi.ac.uk

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

     'medpolish', 'loess', 'locfit', 'plotSpatialEffects',
     'normalizePlates', 'summarizeChannels', 'plateEffects'

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

         data(KcViabSmall)
         x <- KcViabSmall
         xs <- spatialNormalization(x, model="loess", save.model = TRUE)
         ## Calling spatialNormalization function from "normalizePlates":
         xopt <- normalizePlates(x, method="loess", varianceAdjust="none", save.model = TRUE)
         all(xs@rowcol.effects == xopt@rowcol.effects, na.rm=TRUE)

