yeastCC               package:yeastCC               R Documentation

_D_a_t_a _f_r_o_m _t_h_e _S_p_e_l_l_m_a_n _e_t _a_l. (_1_9_9_8) _y_e_a_s_t _c_e_l_l _c_y_c_l_e
_m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     This data package contains an 'exprSet' instance for the yeast
     cell cycle microarray experiment. The dataset contains gene
     expression measures (log-ratios, with Cy3-labeled common
     reference) for 6,178 yeast genes in 77 conditions.

_U_s_a_g_e:

     data(yeastCC)

_D_e_t_a_i_l_s:

     There are four main timecourses: alpha (alpha factor arrest),
     cdc15, cdc28, and elu (elutriation), corresponding to different
     synchronization methods. For details on experimental procedures
     and analysis, refer to Spellman et al. (1998) (in <URL: ../doc>)
     and the Yeast Cell Cycle Analysis Project website (<URL:
     http://genome-www.stanford.edu/cellcycle/>).  The 'exprSet'
     instance 'yeastCC' was derived from the file "combined.txt" on the
     website. The ORF names for the 800 cell cycle regulated genes are
     stored in 'orf800'.

_S_o_u_r_c_e:

     The raw data (images, TIFF) and processed data "combine.txt" used
     to create the 'exprSet' instance 'yeastCC' are available from the
     Yeast Cell Cycle Analysis Project website (<URL:
     http://genome-www.stanford.edu/cellcycle/>).  Gene annotation
     information is available from the Saccharomyces Genome Database
     (SGD, <URL:
     http://genome-www.stanford.edu/Saccharomyces/gene_list.shtml>).
     The script "createYeastCC.R" for generating the 'yeastCC' package
     is available in  <URL: ../doc>.

     Note that 'spYCCES' is an 'ExpressionSet' instance with the same
     data and slightly different phenodata annotation.

_R_e_f_e_r_e_n_c_e_s:

     Spellman et al. (1998). Comprehensive Identification of Cell
     Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by
     Microarray Hybridization. _Molecular Biology of the Cell_, 9:
     3273-3297.

_E_x_a_m_p_l_e_s:

     data(yeastCC)
     yeastCC
     varLabels(yeastCC)
     pData(yeastCC)
     description(yeastCC)
     abstract(yeastCC)
     featureNames(yeastCC)[1:10]
     dim(exprs(yeastCC))

