modifyWeights             package:limma             R Documentation

_m_o_d_i_f_y_W_e_i_g_h_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Modify weights matrix for given gene status values.

_U_s_a_g_e:

     modifyWeights(weights=rep(1,length(status)), status, values, multipliers)

_A_r_g_u_m_e_n_t_s:

 weights: numeric matrix of relative weights, rows corresponding to
          genes and columns to arrays

  status: character vector giving the control status of each spot on
          the array, of same length as the number of rows of 'weights'

  values: character vector giving subset of the unique values of
          'status'

multipliers: numeric vector of same length as 'values' giving factor by
          which weights will be modified

_D_e_t_a_i_l_s:

     The function is usually used to temporarily modify the weights
     matrix during normalization of data. The function can be used for
     example to give zero weight to spike-in ratio control spots during
     normalization.

_V_a_l_u_e:

     Numeric matrix of same dimensions as 'weights' with rows
     corresponding to 'values' in 'status' modified by the specified
     multipliers.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of normalization functions available in LIMMA is given
     in 05.Normalization.

_E_x_a_m_p_l_e_s:

     w <- matrix(runif(6*3),6,3)
     status <- c("Gene","Gene","Ratio_Control","Ratio_Control","Gene","Gene")
     modifyWeights(w,status,values="Ratio_Control",multipliers=0)