filterArray {MmPalateMiRNA} | R Documentation |
RGList
object to remove probes
Filters an RGList
object to remove
probes with foreground
intensities not sufficiently above the background intensity.
Additionally can filter probes based on character strings, to remove
e.g. control probes.
filterArray (obj, ...) ## S4 method for signature 'RGList' filterArray(obj, keep, frac, number, reps)
obj |
An |
keep |
Character vector to be used as a text filter. Only gene names (as
contained in |
frac |
Fraction to use as a background filter. Only those probes with foreground values (both red and green) greater than 'frac' times the background values pass the filter. |
number |
The number of samples required to pass the background filter for each probe. |
reps |
The number of replicates for each probe required to pass the filtering step. |
... |
allows additional arguments to be passed to specific methods |
Returns an RGList
object identical
in structure to the input
object, but with reduced dimension according to the filtering steps.
signature(obj = "RGList")
checkMVs
, fixMVs
,
checkOutliers
, fixOutliers
data(PalateData) reducedSet <- filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"), frac=1.1, number=3, reps=4)