f45cbmk               package:ProData               R Documentation

_A _S_E_L_D_I-_T_O_F _d_a_t_a _o_f _1_6_7 _b_r_e_a_s_t _c_a_n_c_e_r _a_n_d _n_o_r_m_a_l _s_a_m_p_l_e_s _f_r_o_m _t_h_e _M_i_r_o_n _L_a_b_o_r_a_t_o_r_y

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

     The data consist of 167 SELDI-TOF spectra from either individuals 
     with breast cancer or without (normal controls). Two covariates
     are available. The data have been pre-processed by Ciphergen's
     software and the specific details are as follows.  The baselines 
     of the spectra were subtracted using the default parameter 
     settings of the Ciphergen software, and the spectra were 
     normalized by the total ion current normalization function of  the
     Ciphergen software. Peaks were detected with signal to noise 
     ratio (S/N) above 10. Proto-biomarkers, i.e., peaks in each 
     spectrum that have the same M/Z value, were detected with the 
     following parameters: first pass, 10 S/N, min peak threshold  10
     pass, 5 S/N, and add estimated peaks to complete clusters and  it
     is the jointly normalized data that are available here.  The data
     are presented in the form of an 'exprSet' object.

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

     data(f45cbmk)

_F_o_r_m_a_t:

     The different covariates are:

     _G_R_O_U_P: a character vector with four possible  values, "A", "B",
          "C" and "D".  "A" represents HER2  positive patients, "B"
          normal healthy patients, "C"  ER/PR positive patients and "D"
          samples from a single  healthy woman.

     _S_P_E_C_T_R_U_M: a character vector, the spectrum id of  each sample.

_S_o_u_r_c_e:

     Alex Miron's Lab at the Dana-Farber Cancer Institute.

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

     Shi, Q. et al. Biomarker Discovery in Plasma Using Proteomics Ana
     lysis for Early Detection of Breast Cancer. 2004, manuscript.

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

     data(f45cbmk)

