calcW               package:maigesPack               R Documentation

_M_e_t_h_o_d _c_a_l_c_W _t_o _c_a_l_c_u_l_a_t_e _W _v_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generic function 'calcW' to calculate W values from classes of 
     microarray data objects defined in this package.

_U_s_a_g_e:

     calcW(object, ...)

     ## Default S3 method:
     calcW(object, ...)

     ## S3 method for class 'maigesRaw':
     calcW(object, bkgSub="subtract", ...)

_A_r_g_u_m_e_n_t_s:

  object: object of any class. But only some methods are defined in
          this moment.

  bkgSub: character string indicating the type of background
          subtraction. May be 'none', 'subtract', 'half', 'minimum',
          'movingmin', 'edwards', 'normexp' or 'rma'. Uses limma and
          defaults to 'subtract'.

     ...: additional parameters for 'calcW' method.

_D_e_t_a_i_l_s:

     This method receive an object (at moment of class 'maiges',
     'maigesRaw' or 'maigesANOVA') and returns the matrix of W values.
     For objects of class 'maigesRaw' it uses the function
     'backgroundcorrect' from _limma_ package to do background
     correction before the calculation of W values.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_S_e_e _A_l_s_o:

     'backgroundcorrect' in the limma package and 'calcA'.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     calcW(gastro.raw)
     calcW(gastro.norm)

