calcbackground {phyloarray} | R Documentation |
Background values are calculated based on empty spots. The values for non-empty spots are calculated by an interpolation procedure.
calcbackground(datalist, emptyfield="empty")
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. |
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.
The function returns the same object as given in 'datalist', but the
Gb
and Rb
values are replaced by the calculated
background values.
Kurt Sys (kurt.sys@advalvas.be)
# 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)