crosshyb {crosshybDetector}R Documentation

Identify probes affected by crosshybridization

Description

This function identifies probes that are potentially affected by cross-hybridization. The probability of a probe of being a corruptor is computed by Monte Carlo simulations. The algorithm is briefly described into the crosshyb_func help page.

Usage

crosshyb(raw, probeSeq, plate = 1, probeNameID = "ProbeName",
         numPermut = 10000, probes = c("probes", "spike"),
         satValue = 65535, maxProbes = 50, delta = 10)

Arguments

raw an object of class marrayRaw
probeSeq a vector with the probe sequences
plate integer, the array to analyze
probeNameID the slot name of raw containing the probe names. Probes names are extracted with maInfo(maGnames(raw))[[probeNameID]]
numPermut integer, the number of permutations for Monte Carlo simulations
probes the type of probes that are analyzed for potential corruption. Probe types are defined in maControls(raw)
satValue integer, the value corresponding to saturation (default 65535)
maxProbes integer, the maximun number of probes to analyze for potential corruption
delta integer, threshold for difference in melting temperature. Pairs of probes whose delta Tm is lower than delta are considered as similar. Delta Tm i,k is computed as Tm i,i - Tm i,k, where Tm i,i is the Tm of the perfect pairing probe i vs probe i and Tm i,k is the Tm of the imperfect pairing probe i vs probe k

Value

A list containing:

dataR Dataframe with three columns containing the results of the analysis for the putative corruptor probes applied to the red channel. Contains: i) the probe number, ii) the probe name and iii) the pvalue based on Monte Carlo simulations of being a corruptor (pvalue is corrected for multiple testing)
dataG Same as dataR, but applied to the green channel
childrenR A list containing the corrupted probes for each putative corruptor from the red channel
childrenG As childrenR, but applied to the green channel

Author(s)

Paolo Uva

See Also

crosshybMCplot, extractBadProbes, crosshyb_func

Examples

## Not run: 
data(raw)
data(probeSeq)
# This function will take several minutes to finish
crosshyb.out <- crosshyb(raw, probeSeq, plate=1, numPermut=10000, 
                         probeNameID="Name", probes=c("probes", "spike"),
                         satValue = 65535, maxProbes=100)
## End(Not run)

[Package crosshybDetector version 1.0.4 Index]