maNormLoess              package:marray              R Documentation

_I_n_t_e_n_s_i_t_y _d_e_p_e_n_d_e_n_t _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 intensity dependent 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:

     maNormLoess(x="maA", y="maM", z="maPrintTip", w=NULL, subset=TRUE,
     span=0.4, ...)

_A_r_g_u_m_e_n_t_s:

       x: Name of accessor method for spot statistics, usually 'maA'.

       y: Name of accessor method for spot statistics, usually 'maM'.

       z: Name of accessor method for spot statistic used to stratify
          the data, usually a layout parameter, e.g. 'maPrintTip' or
          'maPlate'. If 'z' is not a character, e.g. NULL,  the data
          are not stratified.

       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

_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
     'maLoess', 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.


     Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed (2001).
     Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen,
     A. N. Dorsel, and E. R. Dougherty (eds), _Microarrays: Optical
     Technologies and Informatics_, Vol. 4266 of _Proceedings of SPIE_. 


     Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T.
     P. Speed (2002). Normalization for cDNA microarray data: a robust
     composite method addressing single and multiple slide systematic
     variation. _Nucleic Acids Research_, Vol. 30, No. 4.

_S_e_e _A_l_s_o:

     'maNormMain', 'maLoess', 'loess'.

_E_x_a_m_p_l_e_s:

     # See examples for maNormMain.