AgiMicroRna (version 2.22.0)

RleMicroRna: Relative Log Expression

Description

RLE: Relative Log Expression

Usage

RleMicroRna(object, maintitle, colorfill)

Arguments

object

An expression matrix

maintitle

title of the plot

colorfill

color of the plot

Details

Each Boxplot corresponds to a sample and displays the Relative Log Expression computed for every spot in the array as the difference between the spot intensity and the median intensity for the same feature accros all the arrays. Since majority of the spots are expected not to be differentially expressed, the plot shoud show boxplots centered around zero and all of them having the aproximately the same dispersion. An array showing greater dispersion than the other, or being not centered at zero could have quality problems.

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.

Examples

		data(dd.micro)
                RleMicroRna(log2(dd.micro$meanS),
			maintitle="log2 Mean Signal RLE",
			colorfill="orange")