Description Usage Arguments Details Value Author(s) References See Also Examples
Mimicks the rotation and shearing of raw twocolour intensities performed in Illumina's GenomeStudio. To be performed before any other transformation or normalisation.
1 2 3 4 5 6  shearRawSignal(BSData, plot = FALSE, newFigure = plot,
normOpts = setNormOptions(), maxPlots = 72, ...)
normalizeIllumina(rawData, indTrain = rep(TRUE, length(rawData$x)),
normOpts = setNormOptions(), plot = FALSE, xylim = NULL,
verbose = FALSE)

BSData 

plot 
If 
newFigure 
Logical indicating whether or not to clear the current device before
plotting. If 
normOpts 
List with at least three elements: “nBins”, “minSize”,
and “prob”. See

maxPlots 
Numeric indicating the maximum allowed number of arrays to plot. Exceeding this limit will produce an error 
... 
Additional input parameters to 
rawData 
List containing the numeric vectors “x” and “y” with red and green intensity data for a single array 
indTrain 
Logical index vector specifying which points to base the normalization upon. It may also be a list containing two logical index vectors “10r” and “20g”, containing indexes to all subbead pools with red and green Infinium I beads, respectively. In the latter case, the “10r”points are used to fit the “AA” homozygote asymptote and the “20g”points are used to fit the “BB” homozygote asymptote 
xylim 
If 
verbose 
If 
shearRawSignal
is usually used as a wrapper for
normalizeIllumina
. Even more commonly,
preprocessBeadSet
is used as a wrapper for both.
These functions perform an affine transformation which is similar to in
Illumina's software (Peiffer et al., 2006),
and it differs only in how the homozygote asymptotes are estimated. Both
axes are divided into a number of bins as specified by
normOpts$nBins
. The points specified by
the quantile normOpts$prob
in each bin exceeding
normOpts$minSize
points are used for a least squares fit of
homozygote asymptotes. If normOpts$shearInf1
is TRUE
, only
Infinium I beads are used, and the quantiles are based on all points
in the bins. Otherwise, all points are used, however the quantile is
based on the normOpts$minSize
smallest values only.
In the plot, the red and green lines give the estimated “AA” and “BB” homozygote asymptotes, respectively. The blue dots are the points upon which the rotation and shearing is based.
A "BeadSetIllumina"
object from
shearRawSignal
, or a list containing normalized signal from
normalizeIllumina
. The normalized red and green signal is
transformed such that the “AA” and “BB” homozygotes
asymptotes are perpendicular to each other
Lars Gidskehaug
D. A. Peiffer et al. (2006) Highresolution genomic profiling of chromosomal aberrations using Infinium wholegenome genotyping, Genome Res. 16:11361148
preprocessBeadSet
, setNormOptions
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  #Make artificial, heteroscedastic data
x1 < 5 + exp(rnorm(1000))*100
y1 < 100 + x1*.1 + x1*rnorm(1000,sd=.1)*.2
y2 < 100 + exp(rnorm(1000))*70
x2 < (y25)/10 + (y2100)*rnorm(1000,sd=.1)*.2
rawData < list()
rawData$x < c(x1,x2)
rawData$y < c(y1,y2)
#Affine transformation
normData < normalizeIllumina(rawData,plot=FALSE,verbose=TRUE)
## Not run:
#Affine transformation with plotting
dev.new()
normOpts < setNormOptions(minSize=10)
normData < normalizeIllumina(rawData,normOpts=normOpts,plot=TRUE,verbose=TRUE)
#After rotation and shearing
dev.new()
plot(normData$x,normData$y,pch='.',main='Affine transformation',xlab='R',ylab='G')
abline(v=0,h=0,col='blue')
## End(Not run)

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