maffy.normalize             package:affy             R Documentation

_N_o_r_m_a_l_i_z_e _I_t_e_n_s_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Normalizes feauture intensities from 'AffyBatch's

_U_s_a_g_e:

     maffy.normalize(data,subset,verbose=FALSE,span=0.25,family="symmetric",log.it=TRUE)

_A_r_g_u_m_e_n_t_s:

    data: an matrix of intensities.

  subset: a vector of indexes describing which probes to use for
          normalising.

 verbose: logical value.

    span: See 'loess'.

  family: See 'loess'.

  log.it: logical value.

_D_e_t_a_i_l_s:

     Please refer to references.

_V_a_l_u_e:

     The normalized intensities.

_A_u_t_h_o_r(_s):

     Magnus Astrand

_R_e_f_e_r_e_n_c_e_s:

     Astrand, M. (2003) <URL:
     http://www.math.chalmers.se/~magnusaa/maffy/>

_S_e_e _A_l_s_o:

     'maffy.subset'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)
       x <- pm(Dilution)[1:2000,1:3]
       mva.pairs(x)
       x <- maffy.normalize(x,subset=1:nrow(x))
       mva.pairs(x)
     }

