MuscleExample           package:sigPathway           R Documentation

_S_u_b_s_e_t _o_f _I_n_f_l_a_m_m_a_t_o_r_y _M_y_o_p_a_t_h_y _D_a_t_a_s_e_t _t_o _D_e_m_o_n_s_t_r_a_t_e
_s_i_g_P_a_t_h_w_a_y

_D_e_s_c_r_i_p_t_i_o_n:

     'MuscleExample' is an R workspace containing the following
     objects: (1) 'tab':        a matrix of 5000 rows and 15 columns
     (2) 'phenotype':  a indicator vector which denotes which columns
     in 'tab' are arrays from normal (NORM) and inclusion body myositis
     (IBM) (3) 'G':          a list containing the source, title, and
     the probe set IDs associated with 626 pathways

     The full inflammatory myopathway dataset (which includes all probe
     sets and samples, including more NORM, IBM, and dermatomyositis
     arrays) and a more comprehensive pathway annotation list for the
     HG-U133A and other selected array platforms are available at <URL:
     http://www.chip.org/~ppark/PNAS05/>

     Although the objects contained in 'MuscleExample' are subsets of
     the full dataset, the results obtained from running pathway
     analysis with 'MuscleExample' are comparable to those obtained
     using the full dataset.  This example dataset contains 8 IBM and 7
     NORM arrays. The 5000 probe sets were selected by considering the
     variance of the expression values of each probe set among the 15
     arrays.

_U_s_a_g_e:

     data(MuscleExample)

_F_o_r_m_a_t:

     1 integer matrix, 1 numeric vector, and 1 list

_S_o_u_r_c_e:

     <URL: http://www.chip.org/~ppark/PNAS05/>

_R_e_f_e_r_e_n_c_e_s:

     Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S.,
     Park P.J. (2005)  Discovering statistically significant pathways
     in expression profiling studies.  _Proceedings of the National
     Academy of Sciences of the USA_, *102*, 13544-9.

     <URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102>

