lumiN                  package:lumi                  R Documentation

_B_e_t_w_e_e_n _c_h_i_p _n_o_r_m_a_l_i_z_a_t_i_o_n _o_f _a _L_u_m_i_B_a_t_c_h _o_b_j_e_c_t

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

     A main function of between chip normalization of a LumiBatch
     object. Currently, four methods ("rsn", "loess", "quantile",
     "vsn") are supported.

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

     lumiN(x.lumi, method = c("rsn", "loess", "quantile", "vsn"), ...)

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

  x.lumi: an ExpressionSet inherited object or a data matrix with
          columns as samples and rows as genes

  method: four different between chips normalization methods ("rsn",
          "loess", "quantile", "vsn") are supported 

     ...: other parameters used by corresponding method 

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

     lumiN is an interface for different normalization methods.
     Currently it supports "RSN" (See 'rsn'), "loess" (See
     'normalize.loess'), "quantile" (See 'normalize.quantiles') and
     "VSN" (See 'vsn'). See details in individual functions.

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

     Return an object with expression values normalized. The class of
     the return object is the same as the input object x.lumi. If it is
     a LumiBatch object, it also includes the VST transform function
     and its parameters as attributes: "transformFun", "parameter". See
     'inverseVST' for details.

_N_o_t_e:

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

     Pan Du, Simon Lin

_R_e_f_e_r_e_n_c_e_s:

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

     'rsn'

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

     ## load example data
     data(example.lumi)

     ## Do lumi transform
     lumi.T <- lumiT(example.lumi)

     ## Do lumi between chip normaliazation
     lumi.N <- lumiN(lumi.T, ifPlot=TRUE)

