maNorm2D               package:marray               R Documentation

_2_D _s_p_a_t_i_a_l _l_o_c_a_t_i_o_n _n_o_r_m_a_l_i_z_a_t_i_o_n _f_u_n_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This function is used for 2D spatial location normalization, using
     the robust local regression function 'loess'.  It should be used
     as an argument to the main normalization function 'maNormMain'.

_U_s_a_g_e:

     maNorm2D(x="maSpotRow", y="maSpotCol", z="maM", g="maPrintTip", w=NULL,
     subset=TRUE, span=0.4, ...)

_A_r_g_u_m_e_n_t_s:

       x: Name of accessor method for spot row coordinates, usually
          'maSpotRow'.

       y: Name of accessor method for spot column coordinates, usually
          'maSpotCol'.

       z: Name of accessor method for spot statistics, usually the
          log-ratio 'maM'.

       g: Name of accessor method for print-tip-group indices, usually
          'maPrintTip'.

       w: An optional numeric vector of weights.

  subset: A "logical" or "numeric" vector indicating the subset of
          points used to compute the fits. 

    span: The argument 'span' which controls the degree of smoothing in
          the  'loess' function.

     ...: Misc arguments

_D_e_t_a_i_l_s:

     The spot statistic named in 'z' is regressed on spot row and
     column coordinates, separately within print-tip-group, using the
     'loess' function.

_V_a_l_u_e:

     A function with bindings for the above arguments. This latter
     function takes as argument an object of class '"marrayRaw"' (or
     possibly '"marrayNorm"'), and returns a vector of fitted values to
     be substracted from the raw log-ratios. It calls the function
     'ma2D', which is not specific to microarray objects.

_A_u_t_h_o_r(_s):

     Sandrine Dudoit, <URL: http://www.stat.berkeley.edu/~sandrine>.

_R_e_f_e_r_e_n_c_e_s:

     S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data. In
     G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger,
     editors, _The Analysis of Gene Expression Data: Methods and
     Software_, Springer, New York.

_S_e_e _A_l_s_o:

     'maNormMain', 'ma2D', 'loess'.

_E_x_a_m_p_l_e_s:

     # See examples for maNormMain.