standardNormalization      package:beadarraySNP      R Documentation

_D_e_f_a_u_l_t _c_o_m_p_l_e_t_e _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Performs all steps in normalization at best settings as determined
     in ref.

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

     standardNormalization(snpdata)

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

 snpdata: SnpSetIllumina object with raw data

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

     The function performs in the following steps
     'snpdata<-normalizeBetweenAlleles.SNP(snpdata)'
      'snpdata<-normalizeWithinArrays.SNP(snpdata,callscore = 0.8,
     relative = TRUE,  fixed = FALSE, quantilepersample = TRUE)'
      'snpdata<-normalizeLoci.SNP(snpdata,normalizeTo = 2)'

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

     A 'SnpSetIllumina' object with the 'G, R and intensity' elements
     in  assayData normalized to obtain values close to 2 on a linear
     scale for  unaffected material.

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

     Jan Oosting

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

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

     'normalizeBetweenAlleles.SNP','normalizeWithinArrays.SNP',
     'normalizeLoci.SNP'

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

       data(chr17.260)
       data.nrm<-standardNormalization(chr17.260)

