ProData               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_p_e_c_t_r_a

_D_e_s_c_r_i_p_t_i_o_n:

     This library contains both the raw spectra and the proto-biomarker
      data pre-processed by Ciphergen's software of the 167 samples. 
     Those one hundred and sixty seven samples are collected from 155
     subjects in CPT tubes with plasma isolated and stored in -80C
     until needed. Among the 167 samples, 55 are HER2 positive (A), 64
     are normal healthy women (B), 35 are ER/PR positive (mostly) (C)
     and 13 samples are from a single healthy woman. Samples in group D
     are the only ones from a single subject, all the other samples
     represent draws from individual subjects.  Samples were thawed and
     aliquoted into 100ul vials. The samples were fractionated to
     simplify the proteome into sub-proteomes.  The fractions 4 and 5
     (f45) were processed by the Ciphergen  IMAC protocol with EAM of
     CHCA. 

     Information on the spectrum ID and the pheotype information is
     stored in the 'exprSet' {\tt f45cbmk}, the proto-biomakers
     pre-processed by Ciphergen's software.

     As an alternative, package 'PROcess' may be used for 
     pre-processing of the raw spectra to get a set of
     proto-biomarkers.

_S_o_u_r_c_e:

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

_E_x_a_m_p_l_e_s:

     # plot a raw spectrum
     f45c <- system.file("f45c", package="ProData")
     fs <- dir(f45c,full.names=TRUE)
     plot(read.csv(gzfile(fs[1])), type="l")

     # find out sizes of phenotype groups:
     library(Biobase)
     data(f45cbmk)
     SpecGrp <- pData(f45cbmk)
     table(SpecGrp[,1])

