readIllumina            package:beadarray            R Documentation

_R_e_a_d _B_e_a_d_A_r_r_a_y _i_n_f_o_r_m_a_t_i_o_n _i_n_t_o _R

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

     Uses csv or txt and image files (where available) to load
     information about each array used in a BeadChip or SAM experiment.

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

     readIllumina(arrayNames=NULL, path=".", textType=".txt",
             annoPkg="illuminaProbeIDs", beadInfo=NULL, useImages=TRUE,  
             singleChannel=TRUE, targets=NULL, 
             imageManipulation="sharpen", backgroundSize=17,
             storeXY=TRUE, sepchar="_", dec=".", metrics=FALSE,
             metricsFile="Metrics.txt", backgroundMethod="subtract", 
             offset=0, normalizeMethod="none", ...)

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

arrayNames: character vector containing names of arrays to be read in
          (if present)

    path: character string specifying the location of files to be read
          by the function

textType: character string specifiying the extension of the files which
          store the bead information (ID, x, y, intensities). Typically
          '".txt"' or '".csv"'.

 annoPkg: character string specifying the annotation package  for the
          arrays being read in (only available for certain  expression
          arrays at present).  Default value is '"illuminaProbeIDs"'
          which is not an annotation package, and indicates that
          Illumina bead IDs have been used to identify each bead.

beadInfo: data.frame specifying bead information, such as  probe
          sequence, Illumina ID, etc.

useImages: logical. If TRUE, the foregound and background  values are
          retrieved from the tif images.  When FALSE, the  intensity
          values in the text files are used.  Note that background
          values will not be available (set to 0) when FALSE,  as the
          current option in BeadScan is to store background subtracted
          signals

singleChannel: logical.  Set to TRUE if the data is single  channel
          (Green) or FALSE for two-colour (both Green and Red data)

 targets: data.frame containing sample information

imageManipulation: Currently the only options here are "none" or
          "sharpen", which indicates the Illumina sharpening mask will
          be used prior to foreground averages being calculated

backgroundSize: numeric value which defines the size of the n x n box
          we will use to calculate local background values

 storeXY: logical scalar, indicating whether the xy coordinates should
          be stored

 sepchar: character string which separates row and column in file name
          (default value is '"_"')

     dec: character used in the files for decimal points.  The default
          value is '"."'

 metrics: logical scalar, indicating whether the scanner metrics file
          'metricsFile' is to be read in

metricsFile: name of the scanner metrics file

backgroundMethod: method to use for background correcting the data. 
          Options are '"none"', '"subtract"', '"half"', '"minimum"',
          '"edwards"', '"normexp"' or '"rma"'

  offset: numeric value to add to intensities

normalizeMethod: method to use to normalize the background corrected
          bead-level data. Options are '"none"', '"quantile"' and
          '"vsn"'. Note that the normalization occurs at the bead-level
          and is only available for two-colour data at this stage

     ...: other arguments

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

     This function can be used to read in bead level information using
     the raw ./tif and csv ot txt files output by the scanner. Where
     sample information is available, the 'targets' data.frame can be
     read in using 'read.table'.

     The 'annoFile' contains information on each bead type on the
     array.

     The csv or txt files are used to specify the location and identity
     of each bead on the array and must contain columns for the $x$ and
     $y$ postion of each bead as well as a ProbeID. For two-colour
     arrays, this information is required for each channel.

     The foreground and background intensities of each bead are then
     calculated and stored separately. For foreground calculations the
     sharpening mask used by Illumina is used prior to an averaging
     over the 9 pixels in a 3 x 3 square closest to the bead centre (we
     can choose to calculate the values obtained without this mask).
     For the background intensity we look at the pixels in a 17 x 17
     square and calculate the mean of the 5 lowest values inside this
     square.  If a bead is particularly close to the edge of the image
     then it isn't possible to take a 17 x 17 square for sampling.  In
     this case the background value is taken as the mean of all the
     previous background values and the user is informed that this has
     been done.

     The function creates an BeadLevelList containing foreground and
     background intensities for each bead on each array.

_V_a_l_u_e:

     BeadLevelList object

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

     Mark Dunning, Mike Smith

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

     #BLData = readIllumina()
      
     #targets = read.table("targets.txt", header=T)

     #targets
     #May take a while to run
     #BLData.s = readIllumina(arrayNames=target$Institute.Sample.Label, targets=targets)

     #Create foreground intensities without using sharpening. Should take less time
     #BLData.ns = readIllumina(arrayNames=targets$Institute.Sample.Label, targets=targets, sharpen=FALSE)

     #Use a 9 x 9 are around each bead to calculate the background
     #BLData.ns.9 = readBeadImages(arrayNames=target$Institute.Sample.Label, targets=targets, sharpen=FALSE, backgroundSize=9)

