meeboQualityPlots        package:arrayQuality        R Documentation

_Q_u_a_l_i_t_a_t_i_v_e _d_i_a_g_n_o_s_t_i_c _p_l_o_t _f_o_r _g_e_n_e_r_a_l _h_y_b_r_i_d_i_z_a_t_i_o_n, _s_p_e_c_i_f_i_c
_t_o _M_E_E_B_O _s_e_t.

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

     This function generates diagnostic plots for a qualitative
     assessment of slide quality.

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

     meeboQualityPlots(mrawObj, headerInfo = "", save = TRUE, dev = "png", col = NULL, badspotfunction = NULL, controlId = c("ID", "Name"), seqId = "SeqID", DEBUG = FALSE, ...)

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

 mrawObj: 'marrayRaw'  or 'RGList' object representing the slides to be
          tested.

headerInfo: Text to be used as header in the diagnostic plot.

    save: Logical. If 'TRUE', the plot is saved to a file.

     dev: A "character" string naming the graphics device. This will
          take arguments "png", "jpeg" and "ps" only. By default, dev
          is set to "png".

     col: Vector of colors to use to describe different categories of
          spots.

badspotfunction: Function to use for bad spots on the array.

controlId: Character string. Name of the column of the gpr file used to
          define controls (or provides the name of the probes).

   seqId: A "character" string naming the column of the MEEBO
          annotation to use to retrieve replicated sequences.

   DEBUG: If 'TRUE', debug statements are printed.

     ...: additional arguments

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

     The right panels of the diagnostic plot contain boxplots of the
     various controls in the set, like positive or negative controls,
     as set in the marrayRaw of RGlist object. Replicated controls are
     recognized based on their MEEBO sequence id.

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

     Agnes Paquet

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

     'meeboQuality', 'gpQuality', 'maQualityPlots','MeeboSpotTypes',
     'controlCodeMeebo'

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

     datadir <- system.file("Meebo", package="arrayQuality")
     if (interactive())
     {
     mraw <- read.GenePix(path=datadir, controlcode=controlCodeMeebo)
     meeboQualityPlots(mraw)
     }

