bg.correct.LESN           package:affyPLM           R Documentation

_L_E_S_N - _L_o_w _E_n_d _S_i_g_n_a_l _i_s _N_o_i_s_e _B_a_c_k_g_r_o_u_n_d _c_o_r_r_e_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function background corrects PM probe data using LESN - Low
     End Signal is Noise concepts.

_U_s_a_g_e:

     bg.correct.LESN(object,method = 2,baseline = 0.25, theta=4)

_A_r_g_u_m_e_n_t_s:

  object: an 'AffyBatch'

  method: an integer code specifying which method to use

baseline: A baseline value to use

   theta: A parameter used in the background correction process

_D_e_t_a_i_l_s:

     This method will be more formally documented at a later date.

     The basic concept is to consider that the lowest end of intensites
     is most likely just noise (and should be heavily corrected) and
     the highest end signals are most likely signal and should have
     little adjustment. Low end signals are made much smaller while
     high end signals get less adjustment relative adjustment.

_V_a_l_u_e:

     An 'AffyBatch'

_A_u_t_h_o_r(_s):

     Ben Bolstad bmb@bmbolstad.com

_R_e_f_e_r_e_n_c_e_s:

     Bolstad, BM (2004) _Low Level Analysis of High-density
     Oligonucleotide Array Data: Background, Normalization and
     Summarization_. PhD Dissertation. University of California,
     Berkeley.

_E_x_a_m_p_l_e_s:

     data(affybatch.example)
     affybatch.example.bgcorrect <- bg.correct.LESN(affybatch.example)