stat.ma                 package:sma                 R Documentation

_C_a_l_c_u_l_a_t_i_o_n _o_f _l_o_g _I_n_t_e_n_s_i_t_y _R_a_t_i_o_s _a_n_d _A_v_e_r_a_g_e _l_o_g _I_n_t_e_n_s_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Computes the log intensity ratio M = log_2 (R/G) and the mean log
     intensity A = log_2(R*G)/2, where R and G represent the
     fluorescence intensities in the red and green channels,
     respectively. Logarithms base 2 are used instead of natural or
     decimal logarithms as intensities are typically integers between 1
     and 2^{16}. The log intensity ratios M are normalized using one of
     the five available methods.

_U_s_a_g_e:

     stat.ma(RG, layout, norm="p", pout=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

      RG: a list with 4 elements, each represents a matrix with p rows
          for p genes and n columns for n slides. 
           The first element "R" contains the raw red intensities from
          slide i=1,...,n .
           Similarly, the second element "G" contains the raw green
          intensities. 
           The third element "Rb"  contains the background red
          intensities and 
           the fourth element "Gb" contains the  background green
          intensities.
           This list structure can be generated by the interactive
          function 'init.data'. 

  layout: a list specifying the dimensions of the spot matrix and the
          grid   matrix.  This can be generated by calling 'init.grid'.

    norm: Character string, one of "n", "m", "l", "p" or "s".  This
          argument specifies the type of normalization method to be
          performed: "n" no normalization between the 2 channels; "m"
          'median' normalization, which sets the median of log
          intensity ratios to zero; "l" global 'lowess' normalization;
          "p" print-tip group lowess normalization and "s" scaled
          print-tip group lowess normalization. The default method is
          set to print-tip normalization.

    pout: if TRUE, an M vs. A plot will be produced. Otherwise, a
          matrix of log intensity ratios and average log intensities is
          return.  By default pout is set to FALSE.  The option
          pout='TURE' is not yet implemented.

     ...: other parameters used in 'ma.func'. 

_V_a_l_u_e:

     List containing the following components:

       M: Matrix of log expression ratios M = log_2 (R/G)

       A: Matrix of average log intensities A = log_2(R*G)/2

     For the matrix in each of the components, rows correspond to genes
     and columns correspond to different hybridizations, that is
     different slides.

_N_o_t_e:

     'ma.func', 'norm.l.func', 'norm.scale.func' and 'norm.pin.func'
     are called by 'stat.ma' and are not typically used on their own.

_A_u_t_h_o_r(_s):

     Yee Hwa Yang, yeehwa@stat.berkeley.edu 
      Sandrine Dudoit, sandrine@stat.berkeley.edu 
      Natalie Roberts, nroberts@wehi.edu.au

_R_e_f_e_r_e_n_c_e_s:

     S. Dudoit, Y. H. Yang, M. J. Callow, and T. P. Speed. Statistical
     methods for identifying differentially expressed genes in
     replicated cDNA microarray experiments (Statistics, UC Berkeley,
     Tech Report # 578).

_S_e_e _A_l_s_o:

     'ma.func', 'norm.l.func', 'norm.pin.func', 'norm.scale.func',
     'plot.mva', 'lowess'.

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     ## mouse.setup <- init.grid() 
     ## mouse.data <- init.data() ## see \emph{init.data} 
     mouse.lratio <- stat.ma(mouse.data, mouse.setup)

