calcbackground {phyloarray}R Documentation

Calculate background

Description

Background values are calculated based on empty spots. The values for non-empty spots are calculated by an interpolation procedure.

Usage

  calcbackground(datalist, emptyfield="empty")

Arguments

datalist An object of type phyloarray
emptyfield ID of the spots which are empty, i.e. the spots that are used for background calculation or spots which shouldn't give any signal.

Details

The function calculates the background using an kriging algorithm. It is important to note that only the spots with ID==emptyfield are used and that badspots, i.e. spots with a sd/signal<cutoff are removed from background calculation.

Other or more flexible interpolation procedures might be included in future versions.

Value

The function returns the same object as given in 'datalist', but the Gb and Rb values are replaced by the calculated background values.

Note

Author(s)

Kurt Sys (kurt.sys@advalvas.be)

References

See Also

Scandataraw Phylodata

init.data

plotbackground

krige

Examples

  # load data this-is-escaped-codenormal-bracket33bracket-normal, i.e. this-is-escaped-codenormal-bracket34bracket-normal
  data(Phylodata)

  # histogram of background values before interpolation procedure
  hist(scans$R[,"40"], nclass=50)

  scans <- calcbackground(scans)

  # histogram of background values after interpolation procedure
  hist(scans$R[,"40"], nclass=50)

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