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 _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)      

