qcPlots {AgiMicroRna} | R Documentation

## Plots for Quality Assessment

### 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)

[Package AgiMicroRna version 2.32.0 Index]