genediff               package:LMGene               R Documentation

_R_a_w _p-_v_a_l_u_e _c_a_l_c_u_l_a_t_i_o_n _f_u_n_c_t_i_o_n

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

     Computes two vectors of p-values per gene or probe using
     gene-by-gene ANOVA with individual gene MSE using  both the
     gene-specific MSE and the posterior mean MSE for each term in the
     ANOVA. 
      Assumes a fixed effects model and the correct denominator for all
     comparisons is the MSE.

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

     genediff(eS, model=NULL)

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

      eS: Array data. must be an 'ExpressionSet' object and the
          log-transformation and the normalization of 'exprs(eS)' are
          recommended.

   model: Model used for comparison; see details and 'LMGene'.

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

     The argument 'eS' must be an 'ExpressionSet' object from the
     Biobase package.  If you have a data in a 'matrix' and information
     about the considered factors, then you can use 'neweS' to convert
     the data into an 'ExpressionSet' object. Please see 'neweS' in
     more detail.

     The 'model' argument is an optional character string, constructed
     like the right-hand side of a formula for lm. It specifies which
     of the variables in the 'ExpressionSet' will be used in the model
     and whether interaction terms will be included. If 'model=NULL',
     it uses all variables from the 'ExpressionSet' without
     interactions. Be careful of using interaction terms with factors;
     this often leads to overfitting, which will yield an error.

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

  pvlist: a list containing two sets of p-values obtained by gene
          specific MSE and the posterior MSE methods.

_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:

     'LMGene', 'rowaov'

_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,]

