colonCA               package:colonCA               R Documentation

_D_a_t_a _f_r_o_m _t_h_e _m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t _d_o_n_e _b_y _A_l_o_n _e_t _a_l. (_1_9_9_9)

_D_e_s_c_r_i_p_t_i_o_n:

     The data package contains an exprSet instance for the Alon et al.
     (1999) colon cancer data. 62 samples (40 tumor samples, 22 normal
     samples) from colon-cancer patients were analyzed with an
     Affymetrix oligonucleotide Hum6000 array.

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

     data(colonCA)

_F_o_r_m_a_t:

     Expression set with 2000 genes and 62 samples. 
      There are 3 covariates listed.

        *  'expNr': Number of sample.

        *  'samp': Sample code. 
             positive: Normal tissue, negative: Tumor tissue

        *  'class': Tissue identity. 
             n: Normal tissue, t: Tumor tissue

_D_e_t_a_i_l_s:

     40 samples are from tumors (labelled as "negative") and 22 samples
     are from normal (labelled as "positive") biopsies from healthy
     parts of the colons of the same patients. 
      Two thousand out of around 6500 genes were selected based on the
     confidence in the measured expression levels (for details refer to
     publication). No further preprocessing (normalization etc.) was
     done.

_S_o_u_r_c_e:

     <URL:
     http://microarray.princeton.edu/oncology/affydata/index.html>

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

     U. Alon et al. (1999): Broad patterns of gene expression revealed
     by clustering analysis of tumor and normal colon tissue probed by
     oligonucleotide arrays. _Proc. Natl. Acad. Sci. USA_ *96*,
     6745-6750

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

     library(Biobase)
     data(colonCA)
     xx <- exprs(colonCA)
     dim(xx)
     xx[1:5,1:5]

     colonCA$class
     geneNames(colonCA)[1:20]
     colnames(xx) <- as.character(colonCA$class)
     xx[1:5,1:5]

