init.data {phyloarray}R Documentation

Initialize data

Description

Read the important fields of the several raw data-objects and store them in a new object (with class "phyloarray"). This function also reads the temperatures from the headers.

Usage

  init.data2()

Arguments

Value

The function returns an object of class phyloarray. It is a list with values R (red signal), G (green signal), Rb (red background signal), Gb (green background signal), Rsd (standard deviation of red signal) and Gsd (standard deviation of green signal). The standard deviation values are used to mark bad spots (based on sd/signal). The list contains also X- and Y-values of the spots (to calculate background, if necessary) and the ID's of the probes. Each field R, G, Rb, Gb, Rsd and Gsd is a datamatrix with in the rows the values for the different probes and in the columns the different temperatures. To a larger extent, the columns may be other factors to (such as time-related values), but they are designed to be used for making melting curves and analysis on the melting curves.

Note

Since there is a function init.data in sma, this function has been calles init.data2. It is largely the same function, but some fields are added to make the phylogenetic analysis of melting curves more easy.

Some examples of basic handling of an object of class phyloarray is in the help-file Phylodata

Author(s)

Kurt Sys (kurt.sys@advalvas.be)

References

See Also

Scandataraw Phylodata

read.genepix

getprobes

Examples

  # load the saved raw data from this package:
  # data(Scandataraw)

  # scans <- init.data2()

  # Are you creating a new data matrix or adding new array data
  # to a prexisting data matrix? 
  # Enter "n" for creating  and "a" for adding new array data: n
  # Do the names of all your datasets have the following format: 
  # prefix1, prefix2, prefix3?, ... Here prefix can be any name, 
  # but the suffixes must be integers 1,2, ..., # of arrays. 
  # Enter "y" for yes, "n" for no: y
  # Enter the prefix:scan
  # Enter the number of arrays to be processed:3
  # Enter the name of Cy3 raw data: Gmed
  # Enter the name of Cy3 background: Gbmed
  # Enter the name of Cy3 intensity standard deviation: GSD
  # Enter the name of Cy5 raw data: Rmed
  # Enter the name of Cy5 background: Rbmed
  # Enter the name of Cy5 intensity standard deviation: RSD
  # Enter the name of the ID/probenames field: ID
  # Enter the X values for probe positions: Column
  # Enter the Y values for probe positions: Row
  # Finished creating the dataset.


  # load data this-is-escaped-codenormal-bracket27bracket-normal, i.e. this-is-escaped-codenormal-bracket28bracket-normal
  data(Phylodata)

  names(scans)

  attributes(scans)


[Package phyloarray version 0.1-1 Index]