filterArray: Filter an 'RGList' object to remove probes

Description Usage Arguments Value Methods See Also Examples

Description

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.

Usage

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filterArray (obj, ...)
## S4 method for signature 'RGList'
filterArray(obj, keep, frac, number, reps)

Arguments

obj

An RGList object

keep

Character vector to be used as a text filter. Only gene names (as contained in obj$genes$Name) which contain these text strings will be retained.

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

Value

Returns an RGList object identical in structure to the input object, but with reduced dimension according to the filtering steps.

Methods

signature(obj = "RGList")

See Also

checkMVs, fixMVs, checkOutliers, fixOutliers

Examples

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data(PalateData)
reducedSet <- filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"),
                          frac=1.1, number=3, reps=4) 


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