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", "ssn", "quantile",
     "loess", "vsn") are supported.

_U_s_a_g_e:

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

_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
          ("quantile", "rsn", "ssn", "loess", "vsn") are supported 

 verbose: a boolean to decide whether to print out some messages 

     ...: 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'), "SSN" (See 'ssn'),
     "loess" (See 'normalize.loess'), "quantile" (See
     'normalize.quantiles') and "VSN" (See 'vsn'). See details in
     individual functions. Note: the "VSN" normalization should be
     directly applied to the raw data instead of the lumiT processed
     data.

_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.

_A_u_t_h_o_r(_s):

     Pan Du, Simon Lin

_S_e_e _A_l_s_o:

     'rsn', 'ssn'

_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, method='rsn', ifPlot=TRUE)

