deDGE                 package:edgeR                 R Documentation

_C_o_m_p_u_t_e _m_o_d_e_r_a_t_e_d _d_i_f_f_e_r_e_n_t_i_a_l _e_x_p_r_e_s_s_i_o_n _s_c_o_r_e_s _f_o_r _d_i_g_i_t_a_l _g_e_n_e _e_x_p_r_e_s_s_i_o_n (_D_G_E) _d_a_t_a

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

     Runs weighted likelihood calculation for moderated estimates of
     dispersion, and tests for differences in 'tag' abundance between
     groups

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

      
     deDGE(object,alpha=500,doPoisson=FALSE,verbose=TRUE)

_A_r_g_u_m_e_n_t_s:

  object: 'DGEList' containing elements 'data' (matrix: rows-tags,
          columns-libraries), 'lib.size', 'group' indicating class

   alpha: weight to put on the individual tag's likelihood

doPoisson: logical, whether to fit Poisson model instead of Negative
          Binomial, default 'FALSE'

 verbose: logical, whether to write comments, default 'TRUE'

_V_a_l_u_e:

     'deDGEList' with elements 'ps' (list containing proportion
     estimates), 'r' (estimates of 1/overdispersion), 'pseudo'
     (pseudodata generated by 'quantileAdjust'), 'group' (indicating
     class of each sample), 'M' (geometric mean of library sizes)

_A_u_t_h_o_r(_s):

     Mark Robinson, Davis McCarthy

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

     Robinson MD, Smyth GK. 'Small-sample estimation of negative
     binomial dispersion, with applications to SAGE data.'
     Biostatistics. 2008 Apr;9(2):321-32.

     Robinson MD, Smyth GK. 'Moderated statistical tests for assessing
     differences in tag abundance.' Bioinformatics. 2007 Nov
     1;23(21):2881-7.

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

     # generate raw data from NB, create list object
     y<-matrix(rnbinom(20,size=1,mu=10),nrow=5)
     d<-DGEList(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))

     # find alpha and call main procedure to find differences
     alpha<-alpha.approxeb(d)
     ms<-deDGE(d,alpha=alpha$alpha)

