maNormMain              package:marray              R Documentation

_M_a_i_n _f_u_n_c_t_i_o_n _f_o_r _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 _o_f _c_D_N_A _m_i_c_r_o_a_r_r_a_y _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This is the main function for location and scale normalization of
     cDNA microarray data. Normalization is performed for a batch of
     arrays using location and scale normalization procedures specified
     by the lists of functions 'f.loc' and 'f.scale'. Typically, only
     one function is given in each list, otherwise composite
     normalization is performed using the weights computed by the
     functions 'a.loc' and 'a.scale'. 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"'. Simple wrapper functions are provided by
     'maNorm' and 'maNormScale'.

_U_s_a_g_e:

     maNormMain(mbatch, f.loc=list(maNormLoess()), f.scale=NULL,
     a.loc=maCompNormEq(), a.scale=maCompNormEq(), Mloc=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.

   f.loc: A list of location normalization functions, e.g.,
          'maNormLoess', 'maNormMed', or 'maNorm2D'.

 f.scale: A list of scale normalization functions, .e.g, 'maNormMAD'.

   a.loc: For composite normalization, a function for computing the
          weights used in combining several location normalization
          functions, e.g., 'maCompNormA'.

 a.scale: For composite normalization, a function for computing the
          weights used in combining several scale normalization
          functions.

    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.

_D_e_t_a_i_l_s:

     When both location and scale normalization functions ('f.loc' and
     'f.scale') are passed, location normalization is performed before
     scale normalization. That is, scale values are computed for the
     location normalized log-rations. The same results could be
     obtained by two applications of the function 'maNormMain', first
     with only the location normalization function and 'f.scale=NULL',
     and second with only the scale normalization function and
     'f.loc=NULL'.

_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:

     'maNorm', 'maNormScale', 'maNormLoess', 'maLoess', 'maNormMAD',
     'maMAD', 'maNormMed', 'maMed', 'maNorm2D', 'ma2D', 'maCompNormA',
     'maCompNormEq'.

_E_x_a_m_p_l_e_s:

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

     # Within-print-tip-group loess location normalization of batch swirl
     # - Default normalization
     swirl.norm<-maNormMain(swirl)

     boxplot(swirl.norm)
     boxplot(swirl.norm[,3])
     plot(swirl.norm[,3])

     # Global median normalization for arrays 81 and 82
     swirl.norm <- maNormMain(swirl[,1:2], f.loc = list(maNormMed(x=NULL,y="maM")))

     # Global loess normalization for array 81
     swirl.norm <- maNormMain(swirl[,1], f.loc = list(maNormLoess(x="maA",y="maM",z=NULL)))

     # Composite normalization as in Yang et al. (2002)
     # No MSP controls are available here, so all spots are used for illustration
     # purposes
     swirl.norm <- maNormMain(swirl[,1], f.loc = list(maNormLoess(x="maA",y="maM",z=NULL),maNormLoess(x="maA",y="maM",z="maPrintTip")), a.loc=maCompNormA())