cvArray: Coefficient of variation of replicated probes within array

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Description

Identifies replicated features at probe and at gene level and computes the coefficient of variation of the array

Usage

cvArray(ddDUP, foreground = c("MeanSignal", "ProcessedSignal"),targets,verbose=FALSE)

Arguments

ddDUP	uRNAList, containing the output from readMicroRnaAFE
foreground	Specifies the signal used, only "MeanSignal" or "ProcessedSignal" can be used
targets	data.frame with the target structure
verbose	logical, if TRUE prints out output

Details

In the Agilent microRNA platforms the features are replicated at a probe level and normally, a single microRNA is interrogated by either two or four sets of replicated probes. The replication of the probes allows computing the coefficient of variation (CV) for each array as a measure of the reproducibility of the array. The CV is computed for every set of replicated probes and the CV median is reported as the array CV. A lower array CV indicates a better array reproducibility.

Value

It prints out the results of the replication for the NON CONTROL FEATURES at a probe and gene level.

Author(s)

Pedro Lopez-Romero

Examples

## Not run: 
data(dd.micro)
data(targets.micro)

cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE)

graphics.off()

## End(Not run)

AgiMicroRna documentation built on Nov. 8, 2020, 5:25 p.m.