stat.Chen                package:sma                R Documentation

_A_p_p_l_y _C_h_e_n'_s _s_i_n_g_l_e _s_l_i_d_e _m_e_t_h_o_d

_D_e_s_c_r_i_p_t_i_o_n:

     Applies Chens single slide method.

_U_s_a_g_e:

     stat.Chen(RG,layout,norm="p",image.id=1,pout=TRUE)

_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'.

image.id: Specifies image to which Chen's method will be applied.

    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 with limits due to
          Chen 95% and 99%. If FALSE, returns upper and lower bounds at
          95% and 99% levels.

_V_a_l_u_e:

     List containing the following components:

 lower01: The lower limit of 99% confidence interval

 upper01: The upper limit of 99% confidence interval

 lower05: The lower limit of 95% confidence interval

 upper05: The upper limit of 95% confidence interval

_A_u_t_h_o_r(_s):

     Ben Bolstad, bolstad@stat.berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

     Chen, Y., E.R. Dougherty, and M.L. Bittner. Ratio-based decisions
     and the quantitative analysis of cDNA microarray images. Journal
     of Biomedical Optics , Volume 2 (4), 364-374, 1997. (1997)

_S_e_e _A_l_s_o:

     'stat.ChurSap','stat.Newton'

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     ##mouse.setup <- init.grid() 
     ##mouse.data <- init.data() ## see \emph{init.data}
     stat.Chen(mouse.data,mouse.setup,image.id=3)

