maMAD                 package:marray                 R Documentation

_S_t_r_a_t_i_f_i_e_d _M_A_D _c_a_l_c_u_l_a_t_i_o_n

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

     This function computes the median absolute deviation (MAD) of
     values in 'y' separately within values of 'x'. It is used by
     'maNormMAD' for MAD scale normalization.

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

     maMAD(x, y, geo=TRUE, subset=TRUE)

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

       x: Variables used to stratify the data.

       y: A numeric vector.

     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 MAD. 

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

     A numeric vector of MAD values.

_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', 'maNormMAD', 'mad'.

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

     # See examples for maNormMain.

