interactivePlots {beadarray}R Documentation

Interactive bead level plotting

Description

Plots using bead level data to discover spatial effects and artifacts on arrays

Usage


SAMSummary(BLData, mode="outliers", missing_arrays=NULL, colour=TRUE, scale = NULL,...)
BeadChipSummary(BLData,  mode="outliers",colour=TRUE, scale = NULL,...)

Arguments

BLData BeadLevelList object
mode character string either "outliers", "fg", or "bg" specifying what to display on the plots
scale numeric value giving the amount by which to divide all numbers by (eg for log2 intensities this should be 16) to transform to range 0 - 1
missing_arrays vector of numeric values specifying the index of any arrays that have been removed from the SAM.
colour if TRUE the hexagons will be plotted in colour
... other graphical parameters to plot that can be specified

Details

A plot will be displayed giving a summary of each array in the experiment on the left screen and initially a blank right hand side. The left hand side is coloured according to the number of outliers found on the array or the mean intensity of the array (depending on the mode parameter). Clicking on tha particular array on the left will display a location plot of the outliers or an image plot on the right

See RNews article

Value

Plot will be produced on the current graphical device

Author(s)

Mark Dunning


[Package beadarray version 1.2.2 Index]