colorectal               package:aCGH               R Documentation

_C_o_l_o_r_e_c_t_a_l _a_r_r_a_y _C_G_H _d_a_t_a_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     The colorectal dataset is an object of class 'aCGH'. It represents
     a collection of 124 array CGH profiles of primary colorectal
     tumors and their derived attributes. Each sample was measured on
     the BAC clone DNA microarray with approximate resolution of 1.4 Mb
     per clone. There were approximately 2400 clones spotted on the
     array and each clone was printed in triplicates located
     immediately next to each other. Each array consisted of the 16 (4
     by 4) subarrays. The clones were mapped on the July 03 UCSC
     freeze. There were a number of the discrete and continious
     phenotypes associated with the samples such as age, mutation
     status for various markers, stage, location and so on. All images
     were quantified and normalized by Dr. Taku Tokuyasu using custom
     image software SPOT and postprocessing custom software SPROC.

_U_s_a_g_e:

     data(colorectal)

_S_o_u_r_c_e:

     These data were generated at Dr. Fred Waldman's lab at UCSF Cancer
     Center by K. Nakao and K. Mehta. The manuscript describing the
     data and the analysis are described in High-resolution analysis of
     DNA copy number alterations in colorectal cancer by array-based
     comparative genomic hybridization, _Carcinogenesis_, 2004, Nakao
     et. al.

_R_e_f_e_r_e_n_c_e_s:

     Nakao et. al., High-resolution analysis of DNA copy number
     alterations in colorectal cancer by array-based comparative
     genomic hybridization, _Carcinogenesis_, 2004 Jain et. al, Fully
     automatic quantification of microarray image data, _Genome
     Research_, 2003

_S_e_e _A_l_s_o:

     'aCGH' 'plotGenome'

_E_x_a_m_p_l_e_s:

     data(colorectal)
     ## WARNING: plotting the heatmap takes some time
     plot(colorectal)
     plotGenome(colorectal[,1:2])

