heeboQualityPlots: Qualitative diagnostic plot for general hybridization,...

Description Usage Arguments Details Author(s) See Also Examples

Description

This function generates diagnostic plots for a qualitative assessment of slide quality.

Usage

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heeboQualityPlots(mrawObj, headerInfo = "", save = TRUE, dev = "png",
col = NULL, badspotfunction = NULL, controlId = c("ID", "Name"), seqId =
"SeqID", organism = "Hs", DEBUG = FALSE, ...)

Arguments

mrawObj

marrayRaw or RGList object representing the slides to be tested.

headerInfo

Text to be used as header in the diagnostic plot.

save

Logical. If 'TRUE', the plot is saved to a file.

dev

A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only. By default, dev is set to "png".

col

Vector of colors to use to describe different categories of spots.

badspotfunction

Function to use for bad spots on the array.

controlId

Character string. Name of the column of the gpr file used to define controls (or provides the name of the probes).

seqId

A "character" string naming the column of the MEEBO annotation to use to retrieve replicated sequences.

organism

A "character" string naming the organism genome printed on the array, either "Mm" or "Hs". By default, organism is set to "Hs". It is used to retrieve the corresponding Oligo set annotations.

DEBUG

If 'TRUE', debug statements are printed.

...

additional arguments

Details

The right panels of the diagnostic plot contain boxplots of the various controls in the set, like positive or negative controls, as set in the marrayRaw of RGlist object. Replicated controls are recognized based on their HEEBO sequence id.

Author(s)

Agnes Paquet

See Also

heeboQuality, gpQuality, maQualityPlots,HeeboSpotTypes, controlCodeHeebo

Examples

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if (interactive())
{
require(HEEBOdata)
datadir <- system.file("Heebo", package="HEEBOdata")
gal <- readGAL("hoc.gal", path=datadir)
RG <-
read.maimages(files=c("63421.gpr"), path=datadir, source="genepix.median",other.columns="Flags")
RG$genes <- gal
RG$printer <- getLayout(RG$genes)
RG$genes$Status <- controlStatus(HeeboSpotTypes,RG,verbose=TRUE)
rownames(RG$R) <- rownames(RG$G) <- RG$genes[,"ID"]
heeboQualityPlots(RG)
}


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