heeboQuality          package:arrayQuality          R Documentation

_D_i_a_g_n_o_s_t_i_c_s _p_l_o_t_s _d_e_s_i_g_n_e_d _f_o_r _H_E_E_B_O _s_e_t _c_o_n_t_r_o_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     This component generates several exploratory plots customized to
     the various types of controls provided in the HEEBO set. All
     results are saved as an image. Tested on GenePix format only
     (06-29-2006). For more details about the plots, please refer to
     the HTML description.

_U_s_a_g_e:

     heeboQuality(fnames = NULL, path = ".", galfile = NULL, source
     ="genepix.median", other.columns =
     c("Flags"), controlMatrix=HeeboSpotTypes,controlId = c("ID", "Name"), 
     DOPING = TRUE, heeboSetQC = TRUE, SpotTypeFile = NULL, SpikeTypeFile =
     NULL, cy3col = "Cy3_ng", cy5col = "Cy5_ng", id = "SeqID", namecol =
     c("Symbol", "Name"), annot = NULL, bgMethod = "none", normMethod = "p",
     diagnosticPlot = TRUE, output = TRUE, resdir = ".", dev = "png",
     organism = "Hs", DEBUG = FALSE, ...)

_A_r_g_u_m_e_n_t_s:

  fnames: A "character" string naming the input files.

    path: A "character" string representing the data directory.  By
          default this is set to the current working directory (".").

 galfile: A "character" string naming the file descrining the layout of
          the array. If missing, meeboQuality will read the layour from
          the gpr file.

  source: A "character" string specifing the image analysis program
          which produced the output files. See ?read.maimages in
          package limma for more details.

other.columns: See ?read.maimages in package limma for more details.

controlMatrix: A character matrix of n by 2 or more columns. One column
          should contain a few regular expression of spotted probe
          sequences and another column should contain the corresponding
          control status. By default, controlMatrix is set to
          HeeboSpotTypes.

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

  DOPING: Logical. If 'TRUE', doping controls quality plots are
          generated.

heeboSetQC: Logical. If 'TRUE', mismatch and tiling controls quality
          plots are generated.

SpotTypeFile: A "character" string representing the name of the file
          containing spot type description for the array.

SpikeTypeFile: A "character" string representing the name of the file
          containing doping control information. See HTML description
          for more details.

  cy3col: A "character" string representing the name of the column of
          the SpiketypeFile containing the quantity of each control
          spiked in the Cy3 channel.

  cy5col: A "character" string representing the name of the column of
          the SpiketypeFile containing the quantity of each control
          spiked in the Cy5 channel.

      id: A "character" string describing which column of the MEEBO
          annotation should be used to retrieve replicated oligos, e.g.
          "SeqID".

 namecol: A "character" string describing which column of the
          SpiketypeFile should be used in the legend.

   annot: A "character" string describing which R object should be used
          to look-up probes annotations. By default, it will be set to
          HEEBOset.

bgMethod: Character string specifying which background correction
          method to use. See ?backgroundCorrect in package limma for
          more details.

normMethod: Character string specifying which normalization method
          should be used. See ?normalizeWithinArrays in package limma
          for more details.

diagnosticPlot: Logical. If 'TRUE', a quality diagnostic plot will be
          generated.

  output: Logical. If 'TRUE', normalized M values and A values
          corresponding to the input GenePix files and additionnal
          quality measures are printed to a file.

  resdir: A "character" string representing the directory where the
          results will be saved. By default, this is set to the current
          working directory ("."). 

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

organism: A "character" string naming the organism genome printed on
          the array, either "Mm" or "Hs". By default, organism is set
          to "Hs". 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:

     heeboQuality returns 3 types of quality control plots,
     specifically designed for the various controls offered by the
     HEEBO set. To assess the global performance of an hybridization,
     users can generate a diagnostic plot summarizing several graphs
     and statictics by setting'diagnosticPlot=TRUE'. Then, the
     performance of the HEEBO set can beanalyzed by looking
     specifically at the mismatch and the tiling controls
     ('heeboSetQC=TRUE').

     Finally, we are also providing several exploratory tools to assess
     the performance of the doping-controls ('DOPING=TRUE');these plots
     should be used only if a spike-in mixture was added to the
     hybridization solution.

_V_a_l_u_e:

     heeboquality will produce several graphs, saved in an image file
     format. Please refer to the HTML description for more details. The
     function will also return the MAList object describing your tested
     slides.

_A_u_t_h_o_r(_s):

     Agnes Paquet

_S_e_e _A_l_s_o:

     'heeboQualityPlots', 'gpQuality', 'meeboQuality'

_E_x_a_m_p_l_e_s:

     if (interactive())
     {
     require(HEEBOdata)
     datadir <- system.file("Heebo", package="HEEBOdata")
     MA <-
     heeboQuality(fnames="63421.gpr",galfile="hoc.gal",path=datadir,SpikeTypeFile="DCV2.0June06.txt",cy5col="Cy5_ng",cy3col="Cy3_ng",diagnosticPlot=TRUE, 
     DOPING=TRUE, heeboSetQC=TRUE, namecol="Name", resdir="HeeboQC", DEBUG=TRUE)
     }

