readIntensities          package:arrayMagic          R Documentation

_r_e_a_d_I_n_t_e_n_s_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function takes the 'data.frame' 'slideDescription' as input
     and reads the listed image analysis raw data files of the column
     'slideNameColumn'; cf. function 'readpDataSlides'. Each image
     analysis raw data file must contain tab separated columns and a
     header line - not necessarily at the top of the file; cf. the
     arguments 'removePatterns' and 'skip'. Each file may only contain
     the information for one channel, cf. argument 'channelColumn'. The
     raw data information is returned as an object of class
     'arrayData'. Note: All image analysis quantification (=raw data)
     files have to correspond to the same type of microarray.

_U_s_a_g_e:

     readIntensities(slideDescription, fileNameColumn="fileName", slideNameColumn, channelColumn = NULL, loadPath=".", type = "GenePix", spotAnnoColumns = NULL, dataColumns = NULL, removePatterns = NULL, skip = NULL, spotIdentifier, ..., verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

slideDescription: 'data.frame'; required; default: missing. (cf. the
          return value of the function 'readpDataSlides') The
          'data.frame' must contain at least one column; this column
          has to be named as the argument 'fileNameColumn'. It may
          additionally contain a column named 'slideNameColumn'. 

fileNameColumn: character string; required; default: "fileName".
          'fileNameColumn' specifies the column which contains all
          image quantification result files in the 'data.frame' of
          argument 'slideDescription'.

slideNameColumn: character string; optional; default missing; refers to
          the 'data.frame' of argument 'slideDescription'. If
          'slideNameColumn' is missing the value is set to
          'fileNameColumn'.

channelColumn: named vector of character strings; optional; default
          'NULL'.  If the 'data.frame' of argument 'slideDescription'
          contains information for each channel of every
          slide/hybridisation separately, the 'channelColumn' vector
          contains the column name of the 'data.frame' of argument
          'slideDescription' used to specify the channel. If
          'length(channelColumn) == 1' the character strings "green"
          and "red" are assumed to be used for the coding, otherwise
          'names(channelColumn)' must contain:
          'c("channelColumnName","green","red")'. 

loadPath: character string; required; default: ".". The path is used to
          load the image quantification result files; note: "." refers
          to the working directory. 

spotIdentifier: character string; optional; default missing.
          'spotIdentifier' specifies the column in the image analysis
          result files which contain spot or gene identifiers.

    type: character string; required; possible values: "GenePix",
          "ScanAlyze", "generic" and "genericOneFilePerChannel"; cf.
          Details section. Note: value "generic" requires the arguments
          'spotAnnoColumns', 'dataColumns' and possibly 'skip' and
          'removePatterns', value "genericOneFilePerChannel"
          additionally requires the argument "channelColumn"; whereas
          "GenPix" and "ScanAlyze" use predefined values if not
          otherwise specified; default: "GenePix".

spotAnnoColumns: vector of character strings; the column names of the
          image analysis data file. The columns must contain the same
          information for all files, e.g. the information on the layout
          of the microarray. The argument 'spotIdentifier' is
          automatically added to the vector if not already included;
          default: 'NULL' 

dataColumns: named vector of character strings; the column names of the
          image analysis data file. The columns  contain the raw
          intensities values of each spot;  'names(dataColumns)' must
          contain: 'c("greenForeground", "greenBackground",
          "redForeground", "redBackground")'; default: 'NULL' 

removePatterns: vector of character string(s) each defining a regular
          expression; default: 'NULL'; all lines of each image analysis
          raw data file, which match any of the regular expression(s)
          are discarded. 

    skip: integer; default: 'NULL'; number of lines skipped in each
          image analysis data file; Argument 'skip' applies after all
          lines matched by one of the arguments of 'removePatterns'
          have been discarded. 

     ...: further arguments which are passed to 'read.table'. A
          function which is used inside this function. The arguments
          must not include 'sep',  'header', 'as.is' and 'skip' (for
          'skip' cf. above). 

 verbose: logical; required; default 'TRUE'

_D_e_t_a_i_l_s:

     Details on the argument 'type': 'type="GenePix"' defines 
     'spotAnnoColumns =  c("Block", "Column", "Row", "Name", "ID")' and
     'dataColumns = c("F532.Median", "B532.Median", "F635.Median",
     "B635.Median")' and corresponding 'names(dataColumns) =
     c("greenForeground", "greenBackground", "redForeground",
     "redBackground")', a dynamically determined argument  'skip = 
     grep("Block...Column", imageFile) - 1' and 'removePatterns =
     NULL', whereas 'type="ScanAlyze"' defines 'spotAnnoColumns = c(
     "HEADER", "SPOT", "GRID", "ROW", "COL" )' and 'dataColumns =
     c("CH1I", "CH1B", "CH2I", "CH2B")' and corresponding
     'names(dataColumns) = c("greenForeground", "greenBackground",
     "redForeground", "redBackground")', 'skip = 0' and 'removePatterns
     = c("^REMARK")'.

_V_a_l_u_e:

     object of class 'arrayData'

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'readpDataSlides', 'arrayData-class'

_E_x_a_m_p_l_e_s:

        

      

