DiffAnalysis             package:anapuce             R Documentation

_D_i_f_f_e_r_e_n_t_i_a_l _A_n_a_l_y_s_i_s _f_o_r _p_a_i_r_e_d _d_a_t_a

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

     Performs the differential analysis from normalised paired
     microarray data according to different ways of variance modelling
     and computes lists of differentially expressed genes according
     different multiple testing procedures.

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

     DiffAnalysis(fileIN = "resNorm.txt", n = 3, ind.array = 1:2, name.A = "A", name.M = "M.norm", fileOUT = "ListOfGenes.txt", fileDelete = "GenesOutOfAnalysis.txt", procs = c("bonferroni", "BH"), alpha = c(0.05, 0.05), dyeswap = TRUE, indDS = c(2), fileID = NULL, function.trt = NULL, by.var = "ID", varmixt.meth = FALSE, header = TRUE, sep = "\t", sep.write = "\t", dec.write = ".", ...)

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

fileIN          : normalized data set. 

n               : number of identificant columns. 

ind.array       : the indices of arrays to analyze. 

name.A          : character string containing a regular expression
          contained in the columnames corresponding to the A values. 

name.M          : character string containing a regular expression
          contained in the columnames corresponding to the M values. 

fileOUT         : output data file. 

fileDelete      : output data file containing the list of withdrawn
          genes. 

procs           : adjusting p-values procedures to be used. 

alpha           : values of the first type error to be used in the
          different procedures. 

dyeswap         : logical indicating whether the design is a dye swap. 

indDS           : index of arrays related to dye swap. 

fileID          : file giving information about genes. 

function.trt    : function to be applied before differential analysis. 

by.var          : argument passed to function.trt. 

varmixt.meth    : logical indicating whether to perform the variance
          modelling proposed by Delmar et al. (2005). 

header          : a logical value indicating whether the file contains
          the names of the variables as its first line. Used in the
          read.table function. 

sep             : the field separator string to use in the read.table
          function. 

sep.write       : the field separator string to use in the write.table
          function. 

dec.write       : the string to use for decimal points in the
          write.table function. 

...           : Further arguments to be passed to read.table. 

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

     This function performs a differential analysis in the
     gene-specific and homoscedastic cases. If _varmixt.meth = TRUE_,
     the method used is the method proposed by Delmar et al. (2005),
     (the same as coded in the vm.analysis.paired function from the
     varmixt package.)

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

     By default these following files are created

     - one list of differentially expressed genes by procedure

     - The list of withdrawn genes

     - The list of all the genes

     An R object is returned if function return value is assigned.

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

     J. Aubert

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

     Delmar, P., Robin, S. and Daudin, J.J., (2005), VarMixt: efficient
     variance modelling for the differential analysis of replicated
     gene expression data, _Bioinformatics_, *21*,(4), 502-8

     Dudoit, S., Yang, Y. H., Callow, M. J. and Speed, T.P., (2002),
     Statistical methods for identifying differentially expressed genes
     in replicated cdna microarray experiments, _Statisticia Sinica_,
     *12*, 111-139

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

     'p.adjust',  'MeanBySpot',  'DiffAnalysis.unpaired'

