LMGene                package:LMGene                R Documentation

_L_M_G_e_n_e _m_a_i_n _f_u_n_c_t_i_o_n

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

     LMGene calls function 'genediff' to calculate the raw p-values of
     all genes and then calls function 'pvadjust' to calculate the
     adjusted p-values of all genes. Finally, calls function 'rowlist'
     to list the names of genes that are selected as significant under
     the specified significance level.

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

     LMGene(eS, model=NULL, level = 0.05)

_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: Specifies model to be used. Default is to use all variables
          from eS without interactions. See details.

   level: Significance level 

_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 'level' argument indicates False Discovery Rate, e.g.
     level=0.05 means 5

     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:

   lmres: A list which contains significant gene names for each
          considered factor.

_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', 'pvadjust', 'rowlist'

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

     #library
     library(Biobase)
     library(LMGene)

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

     siggeneslist <- LMGene(LoggedSample, 'patient + dose', 0.01)

