Getting the Total Gene Signal

Description

The function creates an uRNAList containing the TotalGeneSignal computed by the Agilent Feature Extraction software. This signal can be used for the statistical analysis after a possible normalization step.

Usage

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tgsMicroRna(dd, offset, half, makePLOT=FALSE, verbose=FALSE)

Arguments

dd

uRNAList, containing the output from readMicroRnaAFE

offset

integer. To use this option set half = FALSE

half

logical, if TRUE half option is used

makePLOT

logical, if TRUE QC plots with the Total Gene Signal are displayed

verbose

logical, if TRUE prints out some summary results

Details

The function creates a uRNAList oobject that contains in the uRNAList$TGS, uRNAList$TPS, uRNAList$meanS & uRNAList$procS the Total Gene Signal (TGS) as computed by the Agilent Feature Extraction algorithms. This TGS is not in log2 scale. All the replicated genes have the same estimated TGS, and the function simply picks one gene from each set of replicated genes. To mantain the format of the uRNAList, every selected gene retains a probe name attach to them. This probe name is not meaningful any more, since the signal corresponds to the total gene signal and not to the probe signal. The TGS processed by AFE contains some negative values. To get signals with positive values we can either add a positive small constant to all the signals (offset) or we can select the 'half' option, which set to 0.5 all the values that are smaller than 0.5. To use the offset option we have to set half=FALSE, otherwise the half method is used by default. The offset option, adds to each signal the quantity (abs( min(ddTGS$TGS)) + offset), where ddTGS$TGS is the matrix that contains the TotalGeneSignal.

Value

uRNAList containing the TotalGeneSignal computed by the Agilent Feature Extraction software Optionally, it can generate a boxplot, a density plot and a MA plot with the Total Gene Signal.

Author(s)

Pedro Lopez-Romero

References

Agilent Feature Extraction Reference Guide http://www.Agilent.com

Examples

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