maNormMAD               package:marray               R Documentation

_M_A_D _s_c_a_l_e _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 scale normalization using the median
     absolute deviation (MAD) of intensity log-ratios for a group of
     spots. It can be used for within or between array normalization.
     The function should be used as an argument to the main
     normalization function 'maNormMain'.

_U_s_a_g_e:

     maNormMAD(x=NULL, y="maM", geo=TRUE, subset=TRUE)

_A_r_g_u_m_e_n_t_s:

       x: Name of accessor function 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 function for spot statistics, usually 'maM'.

     geo: If 'TRUE', the MAD of each group is divided by the geometric
          mean of the MADs across groups (cf. Yang et al. (2002)). This
          allows observations to retain their original units.

  subset: A "logical" or "numeric" vector indicating the subset of
          points used to compute the scale 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 values used to
     scale the location normalized log-ratios. It calls the function
     'maMAD', 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', 'maMAD', 'mad'.

_E_x_a_m_p_l_e_s:

     # See examples for maNormMain.