MIR-spike-in: Data example

In LVSmiRNA: LVS normalization for Agilent miRNA data

Description

Data from a micro-RNA spike-in experiment, extracted from scanned images using Agilent Feature Extraction Software.

Usage

data("MIR-spike-in")
data("MIR_RA")

Details

This dataset is derived from a library of synthetic RNA sequences, cor- responding to human mature miRNAs as well as in-house miRNAs with particularly similar sequences hybridized on an Agilent Human miRNA Mi- croarray 2.0. Data consist of a total of 799 miRNA species (excluding control features) for 4 samples organized in two groups A and B.

Data, colected with the Agilent Feature Extraction Software, are stored in a RGList object with the following components:

- MIR\$G: 'gMeanSignal' - MIR\$Gb: 'gProcessedSignal' - MIR\$gBGMedianSignal: 'gBGMedianSignal' - MIR\$targets 'targets' - MIR\$Row 'Row' - MIR\$Col 'Column' - MIR\$ProbeUID 'Probe ID' - MIR\$genes\$ControlType 'FLAG to specify the sort of feature' - MIR\$genes\$ProbeName 'Probe Name' - MIR\$genes\$GeneName 'microRNA Name' - MIR\$genes\$SystematicName 'microRNA Name' - MIR\$genes\$Description 'Description (not used)'

MIR.RA holds an object of class RA obtained from using estVC on the example data.

Author(s)

Stefano Calza

References

Willenbrock H, Salomon J, Barken KIMB, Nielsen FC, Litman T. 2009. Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing. RNA 15: 2028-2034.

Data available from Genome Expression Omnibus (GEO) database under the series accession number GSE14511

See Also

read.mir, estVC

LVSmiRNA documentation built on Oct. 31, 2019, 5:29 a.m.