stjd                  package:macat                  R Documentation

_S_u_b_s_e_t _M_i_c_r_o_a_r_r_a_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. (2002)
     The data has been preprocessed using 'vsn' on probe level and the
     probe values have been summed up to probe set values using the
     'median polish' procedure. This is a subset of the data,
     containing only the data for the 5000 probe sets with the highest
     variance across the samples and for 10 exemplary samples, 5 from
     T-lymphocytic Acute Lymphocytic Leukemia (ALL) and 5 from
     B-lymphocytic ALL.

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

     data(stjd)

_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)

_N_o_t_e:

     For the full data package see the Bioconductor data package
     'stjudem'. If it is not already installed on your system, try
     'source("http:\www.bioconductor.org\biocLite.R");
     biocLite("stjudem")'

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

     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.

_S_e_e _A_l_s_o:

     'buildMACAT','stjude' in package 'stjudem' for the complete
     expression data

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

     data(stjd)
     summary(stjd)

