normScaleLimma          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
     _limma_ package.

_U_s_a_g_e:

     normScaleLimma(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 'normalizeBetweenArrays'.

_D_e_t_a_i_l_s:

     This function for scale adjustment is entirely based on function
     'normalizeBetweenArrays' from _limma_ package. See the help page
     for this function to see how to set the parameters. Pay attention
     to the 'vsn' method of scale adjustment, that must be used alone.

_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:

     'normalizeBetweenArrays' from _limma_ package.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## Doing the scale adjustment from median-absolute-value method (from
     ## limma)
     gastro.norm = normScaleLimma(gastro.norm, method="scale")
     boxplot(gastro.norm) ## To see the efect of adjustment

     ## To do VSN scale adjustment (from vsn package) use the command. Be
     ## carefull that this method adjust the variance along A values and not
     ## between chips!!
     gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
     boxplot(gastro.norm) ## See the effect

