maNormScale              package:marray              R Documentation

_S_i_m_p_l_e _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 two basic 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"'. This function can
     be used to conormalize a batch of arrays  ('norm="globalMAD"'
     option).

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

     maNormScale(mbatch, norm=c("globalMAD", "printTipMAD"), subset=TRUE, geo=TRUE,  Mscale=TRUE, echo=FALSE)

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

  mbatch: An 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: A character string specifying the normalization procedures: 

          _g_l_o_b_a_l_M_A_D for global scale normalization using the median
               absolute deviation (MAD), this allows between  slide
               scale normalization

          _p_r_i_n_t_T_i_p_M_A_D for 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.

     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.

  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.

_D_e_t_a_i_l_s:

     See 'maNormMain' for details and 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', 'maNorm'.

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

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

     # Global median normalization followed by global MAD normalization for 
     # only arrays 2 and 3 in the batch swirl

     mnorm1<-maNorm(swirl[,2:3], norm="m")
     mnorm2<-maNormScale(mnorm1, norm="g")

