normalize.invariantset         package:affy         R Documentation

_I_n_v_a_r_i_a_n_t_e _S_e_t _n_o_r_m_a_l_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Normalize arrays in an  'AffyBatch' using an invariant set.

_U_s_a_g_e:

     normalize.AffyBatch.invariantset(abatch,
                        prd.td=c(0.003, 0.007), verbose=FALSE,baseline.type=c("mean","median","pseudo-mean","pseudo-median"),type=c("separate","pmonly","mmonly","together"))

     normalize.invariantset(data, ref, prd.td=c(0.003,0.007))

_A_r_g_u_m_e_n_t_s:

  abatch: an 'AffyBatch'

    data: a vector of intensities on a chip (to normalize to the
          reference).

     ref: a vector of reference intensities.

  prd.td: cutoff parameter (details in the bibliographic reference)

baseline.type: Specify how to determine the baseline array

    type: A string specifying how the normalization should be applied.
          See details for more.

 verbose: A flag to have a dumps throughout the normalization

_D_e_t_a_i_l_s:

     The set of invariant intensities between 'data' and 'ref' is found
     through an iterative process (based on the respective ranks the
     intensities). This set of intensities is used to generate a
     normalization curve by smoothing.

     The 'type' argument should be one of
     '"separate","pmonly","mmonly","together"' which indicates whether
     to normalize only one probe type (PM,MM) or both together or
     separately.

_V_a_l_u_e:

     Respectively a 'AffyBatch' of normalized objects, or a vector of
     normalized intensities, with an attribute "invariant.set" holding
     the indexes of the 'invariant' intensities.

_A_u_t_h_o_r(_s):

     L. Gautier <laurent@cbs.dtu.dk> (Thanks to Cheng Li for the
     discussions about the algorithm.)

_R_e_f_e_r_e_n_c_e_s:

     Cheng Li and Wing Hung Wong, Model-based analysis of
     oligonucleotides arrays: model validation, design issues and
     standard error application. Genome Biology 2001,
     2(8):research0032.1-0032.11

_S_e_e _A_l_s_o:

     'normalize' to normalize 'AffyBatch' objects.