dd.micro: data example (uRNAList)

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

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

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