qcPlots: Plots for Quality Assessment

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

Description

It creates BoxPlots, Density Plots, MA plots, RLE plots and hierachical clustering plots with the sample data set.

Usage

qcPlots(dd, 
	offset, 
	MeanSignal=TRUE, 
	ProcessedSignal=FALSE, 
	TotalProbeSignal=FALSE, 
	TotalGeneSignal=FALSE, 
	BGMedianSignal=FALSE, 
	BGUsed=FALSE, 
	targets)

Arguments

dd	A uRNAList object containing the ouput from readMicroRnaAFE
offset	numeric value to add to the intensities before log transforming
MeanSignal	logical, if TRUE "gMeanSignal" is used
ProcessedSignal	logical, if TRUE "gProcessedSignal" is used
TotalProbeSignal	logical, if TRUE "gTotalProbeSignal" is used
TotalGeneSignal	logical, if TRUE "gTotalGeneSignal" is used
BGMedianSignal	logical, if TRUE "gBGMedianSignal" is used
BGUsed	logical, if TRUE "gBGUsed" is used
targets	data.frame with the target structure

Details

The signals loaded from the AFE data files can be used for the quality assesment using the graphical utilities included in the qcPlots function. For the gMeanSignal, the BoxPlots, Density Plots, MA plots, RLE plots and hierachical clustering plots are done. For the gProcessedSignal the same plots are done, except the hierarchical clustering. For the gTotalProbeSignal and the gTotalGeneSignal only the BoxPlots and Density Plots are done, and finally, for the Background signals only the Boxplots are done.

Author(s)

Pedro Lopez-Romero

References

Boldstad B.M., Collin F., Brettschneider J., Simpson, K., Cope L., Irizarry R. A., Speed T. P. Quality Assesement of Affymetrix GeneChip Data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. (eds.) Gentleman R., Carey V. J., Huber W., Irizarry R. A., Dudoit S. (2005). Springer.

See Also

boxplotMicroRna,plotDensityMicroRna,RleMicroRna, mvaMicroRna and hierclusMicroRna

Examples

## Not run: 
data(dd.micro)
qcPlots(dd.micro,offset=5,
       		MeanSignal=TRUE,
        	ProcessedSignal=TRUE,
        	TotalProbeSignal=TRUE,
        	TotalGeneSignal=TRUE,
        	BGMedianSignal=TRUE,
        	BGUsed=TRUE,
		targets.micro)
graphics.off()


## End(Not run)

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