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", organism = "Mm", 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.

organism: A "character" string naming the organism genome printed on
          the array, either "Mm" or "Hs". By default, organism is set
          to "Mm". It is used to retrieve the corresponding Oligo set
          annotations.

   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:

     if (interactive())
     {
     require(MEEBOdata)
     datadir <- system.file("Meebo", package="MEEBOdata")
     mraw <- read.GenePix(path=datadir)
     maControls(mraw) <- maGenControls(maGnames(mraw),id="ID",controlcode=controlCodeMeebo)
     rownames(maRf(mraw)) <- rownames(maRb(mraw)) <- maGeneTable(mraw)[,"ID"]
     rownames(maGf(mraw)) <- rownames(maGb(mraw)) <- maGeneTable(mraw)[,"ID"]
     meeboQualityPlots(mraw)
     }

