probePlots: Plot the expression profiles of the probes corresponding to...

In EMA: Easy Microarray Data Analysis

Description

Performs expression plots of probes for giver probesets. This function is interesting to show which probes are responsible of intensity signal.

Usage

probePlots(abatch, path, pbsList, labAxisProbes=TRUE, labAxisArrays=TRUE,
legendArrays=TRUE, legendProbes=TRUE, cex.axis=0.9, cex.legend=0.8, pdfName)

Arguments

abatch	An affybatch object.
path	A character. If no affyBatch object, the path where are .CEL files
pbsList	A character. A vector of charcter listing the interesting probesets.
labAxisProbes	A logical. TRUE if probes names have to be plotted in the x axis, FALSE otherwise.
labAxisArrays	A logical. TRUE if arrays names have to be plotted in the x axis, FALSE otherwise.
legendArrays	A logical. TRUE if legend corresponding to the arrays names have to be plotted, FALSE otherwise.
legendProbes	A logical. TRUE if legend corresponding to the probes names have to be plotted, FALSE otherwise.
cex.axis	A numeric. The magnification to be used for x axis relative to the current setting of 'cex'
cex.legend	A numeric. The magnification to be used for legend relative to the current setting of 'cex'
pdfName	A character. Name for a pdf file if needed.

Value

Three plots for each probesets are generated. The first one is an inter chips plot. For each arrays in the AffyBatch, the perfect match intensity of probesets' probes are plotted The second one is an inter probes plot on the perfect match. For each probes in the probeset, the perfect match intensity in each arrays are plotted. The third one is an inter probes plot on the mis match. For each probes in the probeset, the mis match intensity in each arrays are plotted.

Author(s)

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe

Examples

## Not run: 
if (require(affydata)) {
## load example
data(Dilution)
probePlots(Dilution, pbsList=geneNames(Dilution)[1:2])
}

## End(Not run)

EMA documentation built on March 26, 2020, 8:40 p.m.