lymphoma                 package:vsn                 R Documentation

_I_n_t_e_n_s_i_t_y _d_a_t_a _f_o_r _8 _c_D_N_A _s_l_i_d_e_s _w_i_t_h _C_L_L _a_n_d _D_L_B_L _s_a_m_p_l_e_s _f_r_o_m
_t_h_e _A_l_i_z_a_d_e_h _e_t _a_l. _p_a_p_e_r _i_n _N_a_t_u_r_e _2_0_0_0

_D_e_s_c_r_i_p_t_i_o_n:

     8 cDNA chips from Alizadeh lymphoma paper

_U_s_a_g_e:

     data(lymphoma)

_F_o_r_m_a_t:

     'lymphoma' is an 'ExpressionSet' containing the data from 8 chips
     from the lymphoma data set by Alizadeh et al. (see references).
     Each chip represents two samples: on color channel 1 (CH1, Cy3,
     green) the common reference sample, and on color channel 2 (CH2,
     Cy5, red) the various disease samples. See 'pData(lymphoma)'. The
     9216x16 matrix 'exprs(lymphoma)' contains the
     background-subtracted spot intensities (CH1I-CH1B and CH2I-CH2B,
     respectively).

_D_e_t_a_i_l_s:

     The chip intensity files were downloaded from the Stanford
     microarray database. Starting from the link below, this was done
     by following the links _Published Data_ ->  _Alizadeh AA, et al.
     (2000) Nature 403(6769):503-11_ ->  _Data in SMD_ -> _Display
     Data_, and selecting the following  8 slides:

       lc7b019
       lc7b047
       lc7b048
       lc7b056
       lc7b057
       lc7b058
       lc7b069
       lc7b070

     Then, the script 'makedata.R' from the 'scripts' subdirectory of
     this package was run to generate the R data object.

_S_o_u_r_c_e:

     http://genome-www5.stanford.edu/MicroArray/SMD

_R_e_f_e_r_e_n_c_e_s:

     A. Alizadeh et al., Distinct types of diffuse large B-cell 
     lymphoma identified by gene expression profiling. Nature
     403(6769):503-11,  Feb 3, 2000.

_S_e_e _A_l_s_o:

     'vsn'

_E_x_a_m_p_l_e_s:

        data(lymphoma)
        lymphoma
        pData(lymphoma)

