maNorm                package:marray                R Documentation

_S_i_m_p_l_e _l_o_c_a_t_i_o_n _a_n_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 a simple wrapper function around the main
     normalization function 'maNormMain'. It allows the user to choose
     from a set of six basic location and scale normalization
     procedures. The function operates on an object of class
     '"marrayRaw"' (or possibly '"marrayNorm"', if normalization is
     performed in several steps) and returns an object of class
     '"marrayNorm"'.

_U_s_a_g_e:

     maNorm(mbatch, norm=c("printTipLoess", "none", "median", "loess",
     "twoD", "scalePrintTipMAD"), subset=TRUE, span=0.4, Mloc=TRUE,
     Mscale=TRUE, echo=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

  mbatch: Object of class 'marrayRaw', containing intensity  data for
          the batch of arrays to be normalized.  An object of class
          '"marrayNorm"' may also be passed if  normalization is
          performed in several steps.

    norm: Character string specifying the normalization procedures: 

          _n_o_n_e no normalization

          _m_e_d_i_a_n for global median location normalization

          _l_o_e_s_s for global intensity or A-dependent location
               normalization using  the 'loess' function

          _t_w_o_D for 2D spatial location normalization using the  'loess'
               function

          _p_r_i_n_t_T_i_p_L_o_e_s_s for within-print-tip-group intensity dependent
               location  normalization using the 'loess' function

          _s_c_a_l_e_P_r_i_n_t_T_i_p_M_A_D for within-print-tip-group intensity
               dependent  location normalization followed by
               within-print-tip-group scale normalization  using the
               median absolute deviation (MAD). 

               This argument can be specified using the first letter of
               each method. .in -5 

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

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

    Mloc: If 'TRUE', the location normalization values are stored in
          the slot 'maMloc' of the object of class '"marrayNorm"'
          returned by the function, if 'FALSE', these values are not
          retained.

  Mscale: If 'TRUE', the scale normalization values are stored in the
          slot 'maMscale' of the object of class '"marrayNorm"'
          returned by the function, if 'FALSE', these values are not
          retained.

    echo: If 'TRUE', the index of the array currently being normalized
          is printed.

     ...: Misc arguments

_D_e_t_a_i_l_s:

     See 'maNormMain' for details and also more general procedures.

_V_a_l_u_e:

   mnorm: An object of class '"marrayNorm"', containing the normalized
          intensity data.

_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', 'maNormScale'.

_E_x_a_m_p_l_e_s:

     # Examples use swirl dataset, for description type ? swirl
     data(swirl)

     # Global median normalization for swirl arrays 2 and 3
     mnorm<-maNorm(swirl[,2:3], norm="median", echo=TRUE)

     # Within-print-tip-group loess location normalization for swirl array 1
     mnorm<-maNorm(swirl[,1], norm="p", span=0.45)