affySpikeIn               package:DEDS               R Documentation

_G_e_n_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a_s_e_t _f_r_o_m _A_f_f_y_m_e_t_r_i_x _S_p_i_k_e-_i_n _E_x_p_e_r_i_m_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     The spike-in experiment represents a portion of the data used by
     Affymetrix to develop their MAS 5.0 preprocessing algorithm.  Here
     we utilize the RMA (Irizarry et. al) probe level summaries.  The
     data features 14  human genes spiked-in at a series of 14 known
     concentrations  (0, 2^{-2}, 2^{-1}, ..., 2^{10} pM) according to 
     a Latin square design among 12612 null genes.  The data matrix
     'affySpikeIn' represents the two array groups among the 14 array
     groups that contain 12 replicates. Further details are available 
     at <URL:
     http://www.affymetrix.com/analysis/download_center2.affx>.

_U_s_a_g_e:

     data(affySpikeIn)

_V_a_l_u_e:

affySpikeIn: matrix of gene expression levels measurements, rows
          correspond to genes (12626 genes) and columns to 24 samples.

affySpikeIn.L: numeric vector indicating the sample class, 12 (code 0)
          vs. 12 (code 1).

affySpikeIn.gnames: character vecter containing the names of the 12626
          genes.

spikedgene: numeric vector given the location of the 14 spiked genes.

_R_e_f_e_r_e_n_c_e_s:

     R. A. Irizarry, B. M. Bolstad, F. Collin, L. Cope, B. Hobbs and T.
     P. Speed (2003) Summeries of affymetrix genechip probe level data.
     _Nucleic Acide Research_, 31:e15.

