SpikeIn                 package:affy                 R Documentation

_S_p_i_k_e_I_n _E_x_p_e_r_i_m_e_n_t _D_a_t_a: _P_r_o_b_e_S_e_t _E_x_a_m_p_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This 'ProbeSet' represents part of SpikeIn experiment data set.

_U_s_a_g_e:

     data(SpikeIn)

_F_o_r_m_a_t:

     'SpikeIn' is 'ProbeSet' containing the $PM$ and $MM$ intensities
     for a gene spiked in at different concentrations (given in the
     vector 'colnames(pm(SpikeIn))') in 12 different arrays.

_S_o_u_r_c_e:

     This comes from an experiments where 11 different cRNA fragments
     have been added to the hybridization mixture of the GeneChip
     arrays at different pM concentrations.  The 11 control cRNAs were
     BioB-5, BioB-M, BioB-3, BioC-5, BioC-3, BioDn-5 (all {\it E.
     coli}), CreX-5, CreX-3 (phage P1), and  DapX-5, DapX-M, DapX-3
     ({\it B. subtilis}) The cRNA were chosen to match the target
     sequence for each of the Affymetrix control probe sets. For
     example, for DapX (a {\it B. subtilis} gene), the 5', middle and
     3' target sequences (identified by DapX-5, DapX-M, DapX-3) were
     each synthesized separately and spiked-in at a specific
     concentration. Thus, for example, DapX-3 target sequence may be
     added to the total hybridization solution of 200 $mu$l to give a
     final concentration of 0.5 pM.

     For this example we have the $PM$ and $MM$ for BioB-5 obtained
     from the arrays where it was spiked in at 0.0, 0.5, 0.75, 1, 1.5,
     2, 3, 5, 12.5, 25, 50, and 150 pM.

     For more information see Irizarry, R.A., et al. (2001) <URL:
     http://biosun01.biostat.jhsph.edu/~ririzarr/papers/index.html>