normalizeForPrintorder         package:limma         R Documentation

_P_r_i_n_t-_O_r_d_e_r _N_o_r_m_a_l_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Normalize intensity values on one or more spotted microarrays to
     adjust for print-order effects.

_U_s_a_g_e:

     normalizeForPrintorder(object, layout, start="topleft", method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32)
     normalizeForPrintorder.rg(R, G, printorder, method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32, plot = FALSE)
     plotPrintorder(object, layout, start="topleft", slide = 1, method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32)

_A_r_g_u_m_e_n_t_s:

  object: an 'RGList' or 'list' object containing components 'R' and
          'G' which are matrices containing the red and green channel
          intensities for a series of arrays

       R: numeric vector containing red channel intensities for a
          single microarray

       G: numeric vector containing the green channel intensities for a
          single microarray

  layout: list specifying the printer layout, see 'PrintLayout-class'

   start: character string specifying where printing starts in each pin
          group.  Choices are '"topleft"' or '"topright"'.

printorder: numeric vector specifying order in which spots are printed.
          Can be computed from 'printorder(layout,start=start)'.

   slide: positive integer giving the column number of the array for
          which a plot is required

 method : character string, "loess" if a smooth loess curve should be
          fitted through the print-order trend or "plate" if plate
          effects are to be estimated

separate.channels: logical, 'TRUE' if normalization should be done
          separately for the red and green channel and 'FALSE' if the
          normalization should be proportional for the two channels

    span: numerical constant between 0 and 1 giving the smoothing span
          for the loess the curve.  Ignored if 'method="plate"'.

plate.size: positive integer giving the number of consecutive spots
          corresponding to one plate or plate pack.  Ignored if
          'method="loess"'.

    plot: logical. If 'TRUE' then a scatter plot of the print order
          effect is sent to the current graphics device.

_D_e_t_a_i_l_s:

     Print-order is associated with the 384-well plates used in the
     printing of spotted microarrays. There may be variations in DNA
     concentration or quality between the different plates. The may be
     variations in ambient conditions during the time the array is
     printed.

     This function is intended to pre-process the intensities before
     other normalization methods are applied to adjust for variations
     in DNA quality or concentration and other print-order effects.

     Printorder means the order in which spots are printed on a
     microarray. Spotted arrays are printed using a print head with an
     array of print-tips. Spots in the various tip-groups are printed
     in parallel. Printing is assumed to start in the top left hand
     corner of each tip-groups and to proceed right and down by rows,
     or else to start in the top right hand and to proceed left and
     down by rows. See 'printorder' for more details. (WARNING: this is
     not always the case.) This is true for microarrays printed at the
     Australian Genome Research Facility but might not be true for
     arrays from other sources.

     If 'object' is an 'RGList' then printorder is performed for each
     intensity in each array.

     'plotPrintorder' is a non-generic function which calls
     'normalizeForPrintorder' with 'plot=TRUE'.

_V_a_l_u_e:

     'normalizeForPrintorder' produces an 'RGList' containing
     normalized intensities.

     The function 'plotPrintorder' or 'normalizeForPrintorder.rg' with
     'plot=TRUE' returns no value but produces a plot as a side-effect.

     'normalizeForPrintorder.rg' with 'plot=FALSE' returns a list with
     the following components:  

       R: numeric vector containing the normalized red channel
          intensities

       G: numeric vector containing the normalized red channel
          intensites

 R.trend: numeric vector containing the fitted printorder trend for the
          red channel

 G.trend: numeric vector containing the fitted printorder trend for the
          green channe

_A_u_t_h_o_r(_s):

     Gordon Smyth

_R_e_f_e_r_e_n_c_e_s:

     Smyth, G. K. Print-order normalization of cDNA microarrays. March
     2002.  <URL: http://www.statsci.org/smyth/pubs/porder/porder.html>

_S_e_e _A_l_s_o:

     'printorder'.

     An overview of LIMMA functions for normalization is given in
     05.Normalization.

_E_x_a_m_p_l_e_s:

     library(sma)
     data(MouseArray)
     plotPrintorder(mouse.data,mouse.setup,slide=1,separate=TRUE)
     RG <- normalizeForPrintorder(mouse.data,mouse.setup)

