BoutrosRNAi2002             package:nem             R Documentation

_R_N_A_i _d_a_t_a _o_n _D_r_o_s_o_p_h_i_l_a _i_n_n_a_t_e _i_m_m_u_n_e _r_e_s_p_o_n_s_e

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

     Data from a study on innate immune response in {\em Drosophila}
     (Boutros et al, 2002). Selectively removing signaling components
     by RNAi blocked induction of all, or only parts, of the
     transcriptional response to LPS. The nested structure of
     perturbation effects allows to reconstruct a branching in the Imd
     pathway.

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

     data(BoutrosRNAi2002)

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

     BoutrosRNAiExpression: data matrix: 14010 x 16
     BoutrosRNAiDiscrete:   binary matrix:  68 x 16

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

     The dataset consists of 16 Affymetrix-microarrays: 4 replicates of
     control experiments without LPS and without RNAi (negative
     controls), 4 replicates of expression profiling after stimulation
     with LPS but without RNAi (positive controls), and 2 replicates
     each of expression profiling after applying LPS and silencing one
     of the four candidate genes tak, key, rel, and mkk4/hep. 

     'BoutrosRNAiExpression': For preprocessing we performed
     normalization on probe level using a variance  stabilizing
     transformation (Huber et al, 2002), and probe set summarization
     using a median polish fit of an additive model (Irizarry et al,
     2003).

     'BoutrosRNAiDiscrete': contains only the 68 genes more than
     two-fold up-regulated between negative and positive controls. The
     continuous expression values are discretized to '1' (effect:
     closer to negative controls) and '0' (no effect: closer to
     positive controls).

     'BoutrosRNAiDens': log $p$-value density matrix for the 68 genes
     with more than two-fold up-regulated between negative and positive
     controls.

     'BoutrosRNAiLods': B-value matrix for the 68 genes with more than
     two-fold up-regulated between negative and positive controls.

     'BoutrosRNAiLogFC': matrix with log fold changes

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

     Boutros M, Agaisse H, Perrimon N, Sequential activation of
     signaling pathways during innate immune responses in Drosophila.
     Developmental Cell. 3(5):711-722, 2002

_S_e_e _A_l_s_o:

     'nem.discretize'

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

         data("BoutrosRNAi2002")
         dim(BoutrosRNAiExpression)
         dim(BoutrosRNAiDiscrete)      

