imageLimma             package:genArise             R Documentation

_I_m_a_g_e _P_l_o_t _o_f _M_i_c_r_o_a_r_r_a_y

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

     Plot an image of colours representing the log intensity ratio for
     each  spot on the array. This function can be used to explore
     whether there are any spatial effects in the data.

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

     imageLimma(z, row, column, meta.row, meta.column,
     low = NULL, high = NULL)

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

       z: numeric vector or array. This vector can contain any spot
          statistics, such as log intensity ratios, spot sizes or
          shapes, or t-statistics. Missing values  are allowed and will
          result in blank spots on the image 

     row: rows in the microarray 

  column: columns in the microarray 

meta.row: metarows in the microarray

meta.column: metacolumns in the microarray

     low: color associated with low values of 'z'. May be specified as
          a character string  such as '"green"', '"white"' etc, or as a
          rgb vector in which 'c(1,0,0)' is red,  'c(0,1,0)' is green
          and 'c(0,0,1)' is blue. The default value is '"green"' if
          'zerocenter=T' or '"white"' if 'zerocenter=F'.

    high: color associated with high values of 'z'. The default value
          is '"red"' if 'zerocenter=T' or '"blue"' if 'zerocenter=F'.

_N_o_t_e:

     This function is based in the imageplot function from limma
     package.

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

     Gordon K. Smyth (2004) "Linear Models and Empirical Bayes Methods
     for Assessing Differential Expression in Microarray Experiments",
     Statistical Applications in Genetics and Molecular Biology: Vol.
     3: No. 1, Article 3. <URL:
     http://www.bepress.com/sagmb/vol3/iss1/art3>

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

     data(Simon)
     spot.data <- attr(Simon, "spotData")
     M <- log(spot.data$Cy3, 2) - log(spot.data$Cy5, 2)
     imageLimma(z = M, row = 23, column = 24, meta.row = 2, meta.column = 2,
     low = NULL, high = NULL)

