ino                   package:OLIN                   R Documentation

_I_n_t_e_n_s_i_t_y-_d_e_p_e_n_d_e_n_t _n_o_r_m_a_l_i_s_a_t_i_o_n _o_f _t_w_o-_c_o_l_o_u_r _m_i_c_r_o_a_r_r_a_y_s

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

     This functions performs intensity-dependent normalisation based on
     local regression by locfit.

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

     ino(object,alpha=0.3,weights=NA,bg.corr="subtract",...)

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

  object: object of class "marrayRaw" or "marrayNorm" 

   alpha: smoothing parameter

 weights: matrix of weights for  local regression.  Rows correspond to
          the spotted probe sequences, columns to arrays in the batch.
          These may be derived from the matrix of  spot quality weights
          as defined  for "maRaw" objects.

 bg.corr: backcorrection method (for "marrayRaw" objects)  : "none" or
          "subtract"(default).

     ...: Further arguments for 'locfit' function.

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

     The function 'ino' regresses the average logged fold changes (_M_)
     with respect to the average logged spot intensity (_A_). The
     residuals of this fit are the normalised logged fold changes. The
     parameter 'alpha'  specifies the fraction of points that are
     included in the neighbourhood and thus has a value between 0 and
     1. Larger 'alpha' values lead to smoother fits.

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

     Object of class "marrayNorm" with normalised logged ratios

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

     Matthias E. Futschik (<URL:
     http://itb.biologie.hu-berlin.de/~futschik>)

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

     'maNorm', 'locfit.raw','olin', 'oin', 'lin'

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

     # LOADING DATA
       data(sw)

     # INTENSITY-DEPENDENT NORMALISATION
       norm.ino <- ino(sw)

     # MA-PLOT OF NORMALISATION RESULTS OF FIRST ARRAY
       plot(maA(norm.ino)[,1],maM(norm.ino)[,1],main="INO")
      
     # CORRESPONDING MXY-PLOT
        mxy.plot(maM(norm.ino)[,1],Ngc=maNgc(norm.ino),Ngr=maNgr(norm.ino),
                     Nsc=maNsc(norm.ino),Nsr=maNsr(norm.ino),main="INO")

