spotgrid          package:spotSegmentation          R Documentation

_G_r_i_d_d_i_n_g _f_o_r _B_l_o_c_k_s _o_f _M_i_c_r_o_a_r_r_a_y _S_p_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Determines row or column delimiters for spot locations from blocks
     of microarray slide image data.

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

     spotgrid(chan1, chan2, rows = NULL, cols = NULL, span = NULL,
                      show = FALSE)

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

   chan1: matrix of pixel intensities from the first channel.

   chan2: matrix of pixel intensities from the second channel.

    rows: number of spots in a row of the image block.

    cols: number of spots in a column of the image block.

    span: Window size for locating peak signals. This can be of length
          2, in which case the first value is interpreted as a window
          size for the rows and the second as a window size for the
          columns. A default is estimated from the image dimension  and
          number of spots.

    show: logical variable indicating whether or not to display the
          gridding result.

_V_a_l_u_e:

     A list with two elements, 'rowcut' and 'colcut' giving delimiters
     for the row and/or column gridding of the slide. The indexes
     indicate the start of a segment of the grid, except for the last
     one, which indicates the end of the grid.

_R_e_f_e_r_e_n_c_e_s:

     Q. Li, C. Fraley, R. Bumgarner, K. Y. Yeung, and A. Raftery\
     Robust model-based segmentation of microarray images,\  Technical
     Report No.~473, Department of Statistics, University of
     Washington, January 2005.

_S_e_e _A_l_s_o:

     'spotseg'

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

     data(spotSegTest)

     # columns of spotSegTest:
     #  1 intensities from the Cy3 (green) channel
     #  2 intensities from the Cy5 (red) channel

     dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05 

     chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
     chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)

     Grid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)

