arrayWeights              package:limma              R Documentation

_A_r_r_a_y _Q_u_a_l_i_t_y _W_e_i_g_h_t_s

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

     Estimates relative quality weights for each array in a multi-array
     experiment with replication.

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

     arrayWeights(object, design = NULL, weights = NULL)

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

  object: object of class 'numeric', 'matrix', 'MAList', 'marrayNorm',
          'exprSet' or 'PLMset' containing log-ratios or log-values of
          expression for a series of microarrays.

  design: the design matrix of the microarray experiment, with rows
          corresponding to arrays and columns to coefficients to be
          estimated.  Defaults to the unit vector meaning that the
          arrays are treated as replicates.

 weights: optional numeric matrix containing weights for each spot.

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

     The relative reliability of each array is estimated by measuring
     how well the expression values for that array follow the linear
     model.

     A joint mean and dispersion model is fitted to the expression
     values for  each gene by calling the function 'lm.wfit'.  The
     dispersion model  is fitted to the squared residuals from the mean
     fit, and is set up to  have array specific coefficients, which are
     updated in a gene-by-gene manner.  The final estimates of these
     array variances are converted to weights.

     The arguments 'design' and 'weights' will be extracted from the
     data  'object' if available and do not normally need to be set
     explicitly in  the call; if any of these are set in the call then
     they will over-ride  the slots or components in the data 'object'.

     If 'object' is a 'PLMset', then expression values will be taken
     from the slot 'chip.coefs' and weights will be computed from
     'se.chip.coefs'. If 'object' is an 'exprSet', then expression
     values will be taken from the 'exprs' slot, but weights will not
     be computed.

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

     A matrix of array weights, suitable for use in the 'weights'
     argument of 'lmFit'.

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

     Matthew Ritchie

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

     An overview of linear model functions in limma is given by
     5.LinearModels.

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

     ## Not run: 
     array.wts <- arrayWeights(MA, design)
     fit.wts <- lmFit(MA, design, weights=array.wts)
     ## End(Not run)

