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")

