Colon              package:plsgenomics              R Documentation

_G_e_n_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a _f_r_o_m _A_l_o_n _e_t _a_l. (_1_9_9_9)

_D_e_s_c_r_i_p_t_i_o_n:

     Gene expression data (2000 genes for 62 samples) from the
     microarray experiments of Colon tissue samples of Alon et al.
     (1999).

_U_s_a_g_e:

     data(Colon)

_D_e_t_a_i_l_s:

     This data set contains 62 samples  with 2000 genes: 40 tumor
     tissues, coded 2 and 22 normal tissues, coded 1.

_V_a_l_u_e:

     A list with the following elements: 

       X: a (62 x 2000) matrix giving the expression levels of 2000 
          genes for the 62 Colon tissue samples. Each row corresponds
          to a patient, each column to a gene.

       Y: a numeric vector of length 62 giving the type of tissue
          sample (tumor or normal).

gene.names: a vector containing the names of the 2000 genes for the
          gene expression matrix 'X'.

_S_o_u_r_c_e:

     The data are described in Alon et al. (1999) and can be freely
     downloaded from  <URL:
     http://microarray.princeton.edu/oncology/affydata/index.html>.

_R_e_f_e_r_e_n_c_e_s:

     Alon, U. and Barkai, N. and Notterman, D.A. and Gish, K. and
     Ybarra, S. and Mack, D. and Levine, A.J. (1999). Broad patterns of
     gene expression revealed by clustering analysis of tumor and
     normal colon tissues probed by oligonucleotide arrays, Proc. Natl.
     Acad. Sci. USA,*96*(12), 6745-6750.

_E_x_a_m_p_l_e_s:

     # load plsgenomics library
     library(plsgenomics)

     # load data set
     data(Colon)

     # how many samples and how many genes ?
     dim(Colon$X)

     # how many samples of class 1 and 2 respectively ?
     sum(Colon$Y==1)
     sum(Colon$Y==2)

