normalisation            package:anapuce            R Documentation

_F_u_n_c_t_i_o_n _t_o _n_o_r_m_a_l_i_z_e _m_i_c_r_o_a_r_r_a_y _d_a_t_a

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

     Performs the data normalization using a general loess and  a block
     effect correction via the subtraction of the median by block if
     there is a Block column.

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

     normalisation(fileIN = NULL, Red = "F635.Median", Green = "F532.Median", n = 3, flag = -100, graph = TRUE, filter.function = filterByDefault, filter.fic = NULL, filter.var = NULL, sep.write = "\t", dec.write = ".", header = TRUE, sep = "\t", skip = 0, ...)

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

fileIN          : on optional regular expression contained in names of
          the files to analyze

Red             : name of the column containing the Cy5 values

Green           : name of the column containing the Cy3 values 

n               : number of identificant columns 

flag            : list of flags values to delete 

graph           : logical indicating wether to perform graphics 

filter.function : function to perform before beginning the
          normalization 

filter.fic      : argument passed to filter.funtion - file containing
          the values of the variable named _filter.var_ to delete 

filter.var      : argument passed to filter.funtion 

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 

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 

skip            : integer: the number of lines of the data file to skip
          before beginning to read data. 

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

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

     By default _fileIN=NULL_ and the files to analyze have to be
     choosen among all the files in the working directory.  If fileIN
     is not NULL, only file names which match the regular expression
     fileIN will be proposed to the normalization step.

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

     A file _resNorm.txt_ containing the normalized data and if
     _graph=TRUE_ a file .pdf per array with graphics

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

     J. Aubert

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

     Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J. and
     Speed, T., (2002), Normalization for cDNA microarray data: a
     robust composite method addressing single and multiple slide
     systematic variation, _Nucleic Acids Research_ *30*.

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

     'filterByDefault','read.table'

