normLoc              package:maigesPack              R Documentation

_N_o_r_m_a_l_i_s_e _a _c_D_N_A _M_i_c_r_o_a_r_r_a_y _O_b_j_e_c_t

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

     This function loads a 'maigesRaw' object and corrects for location
     bias.

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

     normLoc(obj=NULL, ...)

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

     obj: object of type 'maigesRaw' to be normalised.

     ...: additional parameters for function 'normalizeWithinArrays'
          from _limma_ package.

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

     This function for normalisation is entirely based on the function
     'normalizeWithinArrays' from _limma_ package. See their help page
     to known how to setup the parameters correctly. The parameters
     'layout' and 'weights', are automatically specified by the object
     'obj' and must not be specified.

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

     This function returns a 'maiges' object.

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

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

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

     'normalizeWithinArrays' from _limma_ package.

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

     ## Loading the dataset
     data(gastro)

     ## Do the normalization by loess method and span 0.4
     gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess")

     ## Do the same normalization without background subtraction
     gastro.norm = normLoc(gastro.raw2, span=0.4, method="loess", bc.method="none")

