stjude                package:stjudem                R Documentation

_M_i_c_r_o_a_r_r_y _D_a_t_a _f_r_o_m _S_t._J_u_d_e _C_h_i_l_d_r_e_n _R_e_s_e_a_r_c_h _H_o_s_p_i_t_a_l (_U_S_A)

_D_e_s_c_r_i_p_t_i_o_n:

     Example for list-structure used by many functions in MACAT. It's
     based on the gene expression data published by Yeoh et al. in
     2002.[Yeoh et al. Classification,  subtype discovery, and
     prediction of outcome in pediatric acute  lymphoblastic leukemia
     by gene expression profiling. Cancer Cell.  March 2002. 1:
     133-143. The data has been preprocessed using 'vsn' on probe level
     and the probes have been summed up using 'median polish'.

_U_s_a_g_e:

     data(stjude)

_F_o_r_m_a_t:

     List of class 'MACATData' with 6 components:

     _g_e_n_e_N_a_m_e: Identifiers of genes/probe sets in expression data

     _g_e_n_e_L_o_c_a_t_i_o_n: Location of genes on their chromosome as distance
          from 5'end in base pairs Negative numbers denote genes on the
          antisense strand.

     _c_h_r_o_m_o_s_o_m_e: Chromosome of the respective gene. Components
          'geneName', 'geneLocation', and 'chromosome' are in the same
          order.

     _e_x_p_r: expression matrix with rows = genes and columns =
          samples/patients

     _l_a_b_e_l_s: (disease) subtype of each sample, has length = number of
          columns of expression matrix

     _c_h_i_p: Identifier for Microarray used for the experiments (here for
          the Affymetrix HG-U95av2 Oligonucleotide GeneChip)

_S_o_u_r_c_e:

     Yeoh et al. Classification,  subtype discovery, and prediction of
     outcome in pediatric acute  lymphoblastic leukemia by gene
     expression profiling. Cancer Cell.  March 2002. 1: 133-143.

_E_x_a_m_p_l_e_s:

     data(stjude)
     summary(stjude)

