normaliseIllumina {beadarray} | R Documentation |
Normalises expression intensities so that the intensities are comparable between arrays.
normaliseIllumina(BSData, method="quantile", transform="none", T=NULL)
BSData |
an 'ExpressionSetIllumina' object |
method |
character string specifying normalisation method
(options are "quantile" , "qspline" , "vsn" ,
"rankInvariant" , "median" and "none" . |
transform |
character string specifying transformation to apply
to the data (options are "none" , "log2" and "vst" |
T |
A target distribution vector used in "rankInvariant"
normalisation. If NULL , the mean is used. |
Normalisation is intended to remove from the expression measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.
When transform="vst"
the variance stabilising transformation
from the 'lumi' package is applied to the data. Refer to the 'lumi'
documentation for further particulars.
For further particulars on the different normalisation methods options
refer to the individual help pages (?normalize.quantiles
for
"quantile"
, ?normalize.qspline
for "qspline",
?rankInvariantNormalise
for "rankInvariant"
,
?medianNormalise
for "median"
and ?vsn2
for "vsn"
.
For median normalisation, the intensity for each gene is adjusted by subtracting the median of all genes on the array and then adding the median across all arrays. The effect is that each array then has the same median value.
Note: If your BSData
object contains data already on the
log-scale, be careful that you choose an appropriate transform
to avoid logging it twice. The same applies for the "vst"
transformation and "vsn"
normalisation methods which require
the expression data stored in BSData
to be on the original
(un-logged) scale.
An 'ExpressionSetIllumina' object which conatains the transformed and normalised expression values for each array.
Matt Ritchie
data(BSData) BSData.norm = normaliseIllumina(BSData, method="quantile", transform="log2")