read.maimages             package:limma             R Documentation

_R_e_a_d _R_G_L_i_s_t _f_r_o_m _I_m_a_g_e _A_n_a_l_y_s_i_s _O_u_t_p_u_t _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads an RGList from a series of two-color microarray image
     analysis output files

_U_s_a_g_e:

     read.maimages(files=NULL,source="generic",path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,annotation=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote=NULL,...)
     read.imagene(files,path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...)

_A_r_g_u_m_e_n_t_s:

   files: character vector giving the names of the files containing
          image analysis output or, for Imagene data, a character
          matrix of names of files. If omitted, then all files with
          extension 'ext' in the specified directory will be read in
          alphabetical order.

  source: character string specifying the image analysis program which
          produced the output files.  Choices are '"generic"',
          '"agilent"', '"arrayvision"', 'arrayvision.ARM"',
          'arrayvision.MTM"', '"bluefuse"', '"genepix"',
          '"genepix.custom"', '"genepix.median"', '"imagene"',
          '"quantarray"', '"scanarrayexpress"', '"smd.old"', '"smd"',
          '"spot"' or '"spot.close.open"'.

    path: character string giving the directory containing the files.
          The default is the current working directory.

     ext: character string giving optional extension to be added to
          each file name

   names: character vector of names to be associated with each array as
          column name. Defaults to 'removeExt(files)'.

 columns: list with fields 'R', 'G', 'Rb' and 'Gb' giving the column
          names to be used for red and green foreground and background
          or, in the case of Imagene data, a list with fields 'f' and
          'b'.  This argument is optional if 'source' is specified,
          otherwise it is required.

other.columns: character vector of names of other columns to be read
          containing spot-specific information

annotation: character vector of names of columns containing annotation
          information about the probes

  wt.fun: function to calculate spot quality weights

 verbose: logical, 'TRUE' to report each time a file is read

     sep: the field separator character

   quote: character string of characters to be treated as quote marks

     ...: any other arguments are passed to 'read.table'

_D_e_t_a_i_l_s:

     This is the main data input function for the LIMMA package for
     two-color microarray data. It extracts the foreground and
     background intensities from a series of files, produced by an
     image analysis program, and assembles them into the components of
     one list. The image analysis programs Agilent Feature Extraction,
     ArrayVision, BlueFuse, GenePix, ImaGene, QuantArray (Version 3 or
     later), Stanford Microarray Database (SMD) and SPOT are supported
     explicitly. Data from some other image analysis programs can be
     read if the appropriate column names containing the foreground and
     background intensities are specified using the 'columns' argument.
     (This will work if the column names are unique and if there are no
     rows in the file after the last line of data. Header lines are
     ok.)

     SMD data should consist of raw data files from the database, in
     tab-delimited text form. There are two possible sets of column
     names depending on whether the data was entered into the database
     before or after September 2003. 'source="smd.old"' indicates that
     column headings in use prior to September 2003 should be used. In
     the case of GenePix, two possible foreground estimators are
     supported: 'source="genepix"' uses the mean foreground estimates
     while 'source="genepix.median"' uses median foreground estimates.
     GenePix 6.0 and later also supplies some custom background
     options, notably morphological background. If the GPR files have
     been written using a custom background, you may read it using
     'source="genepix.custom"'.  In the case of SPOT, two possible
     background estimators are supported: if 'source="spot.close.open"'
     then background intensities are estimated from 'morph.close.open'
     rather than 'morph'.

     Spot quality weights may be extracted from the image analysis
     files using a weight function wt.fun. 'wt.fun' may be any
     user-supplied function which accepts a data.frame argument and
     returns a vector of non-negative weights. The columns of the
     data.frame are as in the image analysis output files. There is one
     restriction, which is that the column names should be refered to
     in full form in the weight function, i.e., do not rely on name
     expansion for partial matches when refering to the names of the
     columns. See 'QualityWeights' for suggested weight functions.

     For Imagene image data the argument 'files' should be a matrix
     with two columns. The first column should contain the names of the
     files containing green channel (cy3) data and the second column
     should contain names of files containing red channel (cy5) data.
     If 'source="imagene"' and 'files' is a vector of even length
     instead of a matrix, then each consecutive pair of file names is
     assumed to correspond to the same array. The function
     'read.imagene' is called by 'read.maimages' when
     'source="imagene"'. It does not need to be called directly by
     users.

     ArrayVision reports spot intensities in a number of different
     ways. 'read.maimages' caters for ArrayVision's Artifact-removed
     (ARM) density values as '"arrayvision.ARM"' or for Median-based
     Trimmed Mean (MTM) density values as '"arrayvision.MTM"'.
     ArrayVision users may find it useful to read the top two lines of
     their data file to check which version of density values they
     have.

     The argument 'other.columns' allows arbitrary columns of the image
     analysis output files to be preserved in the data object. These
     become matrices in the component 'other' component. For ImaGene
     data, the other column headings with be prefixed with '"R "' or
     '"G "' as appropriate.

_V_a_l_u_e:

     An 'RGList' object containing the components 

       R: matrix containing the red channel foreground intensities for
          each spot for each array.

      Rb: matrix containing the red channel background intensities for
          each spot for each array.

       G: matrix containing the green channel foreground intensities
          for each spot for each array.

      Gb: matrix containing the green channel background intensities
          for each spot for each array.

 weights: spot quality weights, if 'wt.fun' is given

   other: list containing matrices corresponding to 'other.columns' if
          given

   genes: data frame containing annotation information about the
          probes, for example gene names and IDs and spatial positions
          on the array, currently set only if 'source' is '"agilent"',
          '"genepix"' or 'source="imagene"' or if the 'annotation'
          argument is set

 targets: data frame with column 'FileName' giving the names of the
          files read

  source: character string giving the image analysis program name

 printer: list of class 'PrintLayout', currently set only if
          'source="imagene"'

_W_a_r_n_i_n_g_s:

     All image analysis files being read are assumed to contain data
     for the same genelist in the same order. No checking is done to
     confirm that this is true. Probe annotation information is read
     from the first file only.

_A_u_t_h_o_r(_s):

     Gordon Smyth, with speed improvements by Marcus Davy

_R_e_f_e_r_e_n_c_e_s:

     Web pages for the image analysis software packages mentioned here
     are listed at <URL: http://www.statsci.org/micrarra/image.html>

_S_e_e _A_l_s_o:

     'read.maimages' is based on 'read.table' in the base package.
     'read.marrayRaw' is the corresponding function in the marray
     package.

     An overview of LIMMA functions for reading data is given in
     03.ReadingData.

_E_x_a_m_p_l_e_s:

     #  Read all .gpr files from current working directory
     #  and give weight 0.1 to spots with negative flags

     ## Not run: 
     files <- dir(pattern="*\\.gpr$")
     RG <- read.maimages(files,"genepix",wt.fun=wtflags(0.1))
     ## End(Not run)

     #  Read all .spot files from current working director and down-weight
     #  spots smaller or larger than 150 pixels

     ## Not run: 
     files <- dir(pattern="*\\.spot$")
     RG <- read.maimages(files,"spot",wt.fun=wtarea(150))
     ## End(Not run)

