dd.micro {AgiMicroRna} | R Documentation

## data example (uRNAList)

### Description

Data, extracted from scanned images using Agilent Feature Extraction Software, are stored in a uRNAList object.

### Usage

    data(dd.micro)

### Details

A data example is provided. The data example includes 3 experimental conditions with two replicates.

For these data, chips were scanned using the Agilent G2567AA Microarray Scanner System (Agilent Technologies) Image analysis and data collection were carried out using the Agilent Feature Extraction 9.1.3.1. (AFE).

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

uRNAList\$TGS

  matrix, 'gTotalGeneSignal'

uRNAList\$TPS

  matrix, 'gTotalProbeSignal'

uRNAList\$meanS

  matrix, 'gMeanSignal'

uRNAList\$procS

  matrix, 'gProcessedSignal'

uRNAList\$targets

  data.frame, 'FileName'

uRNAList\$genes\$ProbeName

  vector of characters, 'AGilent Probe Name'

uRNAList\$genes\$GeneName

  vector of characters, 'microRNA Name'

uRNAList\$genes\$ControlType

  vector of integers, '0'= Feature, '1'= Positive control, '-1'= Negative control

uRNAList\$other\$gIsGeneDetected

  matrix, FLAG to classify signal if 'IsGeneDetected=1' or 'not=0'

uRNAList\$other\$gIsSaturated

  matrix, FLAG to classify signal if 'IsSaturated = 1' or 'not=0'

uRNAList\$other\$gIsFeatPopnOL

  matrix, FLAG to classify signal if 'IsFeatPopnOL = 0' or 'not=1'

uRNAList\$other\$gIsFeatNonUnifOL

  matrix, FLAG to classify signal if 'gIsFeatNonUnifOL = 0' or 'not=1'

uRNAList\$other\$gBGMedianSignal

  matrix, gBGMedianSignal

uRNAList\$other\$gBGUsed

  matrix, gBGUsed

### Author(s)

Pedro Lopez-Romero

### See Also

`readMicroRnaAFE.Rd`

[Package AgiMicroRna version 2.36.0 Index]