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)

