maNormMed               package:marray               R Documentation

_M_e_d_i_a_n _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 location normalization using the median
     of  intensity log-ratios for a group of spots. The function should
     be used  as an argument to the main normalization function
     'maNormMain'.

_U_s_a_g_e:

     maNormMed(x=NULL, y="maM", subset=TRUE)

_A_r_g_u_m_e_n_t_s:

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

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

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

_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  subtracted from the raw log-ratios. It calls the function
     'maMed',  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', 'maMed', 'median'.

_E_x_a_m_p_l_e_s:

     # See examples for maNormMain.