RLE            package:Agi4x44PreProcess            R Documentation

_R_e_l_a_t_i_v_e _L_o_g _E_x_p_r_e_s_s_i_o_n

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

     RLE: Relative Log Expression

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

     RLE(object, maintitle, colorfill)

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

  object: An expression matrix, in log2 scale  

maintitle: title of the plot  

colorfill: color of the plot  

_D_e_t_a_i_l_s:

     Each Boxplot corresponds to a sample and displays the Relative Log
     Expression computed for every spot in the array as the difference
     between the spot intensity and the median intensity for the same
     feature accros all the arrays. Since  majority of the spots are
     expected not to be differentially expressed, the plot shoud show
     boxplots centered around zero and all of them having the
     aproximately the same dispersion.  An array showing greater
     dispersion than the other, or  being not centered at zero could
     have quality problems.

_A_u_t_h_o_r(_s):

     Pedro Lopez-Romero

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

     Boldstad B.M., Collin F., Brettschneider J., Simpson, K., Cope L.,
     Irizarry R. A., Speed T. P. Quality Assesement of Affymetrix
     GeneChip Data. In Bioinformatics and Computational Biology
     Solutions Using R and Bioconductor. (eds.)  Gentleman R.,  Carey
     V. J., Huber W., Irizarry R. A., Dudoit S. (2005). Springer.

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

     ## Not run: 
                     data(dd)
                     maintitle="RLE example "
                     colorfill="orange"
                     RLE(log2(dd$G),maintitle,colorfill)
     ## End(Not run)

