RleMicroRna: Relative Log Expression

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

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.

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.

Examples

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

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