normScaleMarray          package:maigesPack          R Documentation

_S_c_a_l_e _a_d_j_u_s_t _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' or 'maiges' object and scale
     adjust (normalise between arrays) the data using functions from
     _marray_ package.

_U_s_a_g_e:

     normScaleMarray(obj=NULL, ...)

_A_r_g_u_m_e_n_t_s:

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

     ...: additional parameters for function 'maNormScale'.

_D_e_t_a_i_l_s:

     This function for scale adjustment is entirely based on function
     'maNormScale' from _marray_ package. See the help page for this
     function to see how to set the parameter. Pay attention to the
     'subset' argument that is fixed directly from the 'UseSpots' and
     'BadSpots' from 'obj' object, and must not be specified in the
     additional arguments.

     The functionality of the scale adjustment function from _marray_
     package was added because it uses an estimator of MAD different
     from that one used in _limma_ package. Also, using  'maNormScale'
     function it is possible to do print tip scale adjustment.

_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:

     'maNormScale' from _marray_ package.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Doing global MAD scale adjustment
     gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD")
     boxplot(gastro.norm) ## To see the effect of MAD adjustment

     ## For print tip MAD use the following command
     ## Not run: 
     gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD")
     ## End(Not run)

