pvadjust               package:LMGene               R Documentation

_P-_v_a_l_u_e _a_d_j_u_s_t_i_n_g _f_u_n_c_t_i_o_n

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

     This function converts the given raw p-values into the FDR
     adjusted p-values using R package 'multtest'.

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

     pvadjust(pvlist)

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

  pvlist: A list containing raw p-values 

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

     'pvlist' is the output from 'genediff' containing p-values from
     gene-specific MSE's and posterior MSE's.

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

pvlist2 : A list with the raw p-values and the newly computed FDR
          adjusted p-values

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

     David Rocke and Geun-Cheol Lee

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

     David M. Rocke (2004), Design and analysis of experiments with
     high throughput biological assay data, Seminars in Cell &
     Developmental Biology, 15, 703-713. 

     <URL: http://www.idav.ucdavis.edu/~dmrocke/>

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

     'genediff'

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

     #library
     library(Biobase)
     library(LMGene)

     #data
     data(sample.mat)
     data(vlist)
     LoggedSmpd0<-neweS(lnorm(log(sample.mat)),vlist)

     pvlist<-genediff(LoggedSmpd0)
     pvlist$Posterior[1:5,]

     apvlist<-pvadjust(pvlist)
     names(apvlist)
     apvlist$Posterior.FDR[1:5,]

