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
     Analysis for Early Detection of Breast Cancer. 2004, manuscript.

_E_x_a_m_p_l_e_s:

     data(f45cbmk)

