preprocess {Ringo} | R Documentation |
Calls one of various limma
functions to transform raw probe
intensities into (background-corrected) normalized log ratios
(M-values).
preprocess(myRG, method = "vsn", returnMAList=FALSE, verbose=TRUE, ...)
myRG |
object of class RGList |
method |
string; denoting which normalization method to choose |
returnMAList |
logical; should an MAList object be returned? Default is to return an ExpressionSet object. |
verbose |
logical; progress output to STDOUT? |
... |
further arguments to be passed on
normalizeWithinArrays and normalizeBetweenArrays |
The procedure and called limma
functions depend on the choice of
method.
limma
's function backgroundCorrect
with
method="normexp"
and offset=50
. Then calls
normalizeWithinArrays
.normalizeBetweenArrays
with method="vsn"
.normalizeBetweenArrays
with method="Gquantile"
.limma
's function backgroundCorrect
with
method="normexp"
and offset=50
. Then calls
normalizeWithinArrays
with method="median".
log2(R)-log2(G)
as component M
and (log2(R)+log2(G))/2
as component A
;
uses normalizeWithinArrays
with method="none"
.
Returns normalized, transformed values as an object of class
ExpressionList
or MAList
.
Joern Toedling toedling@ebi.ac.uk
backgroundCorrect
,
normalizeWithinArrays
,
normalizeBetweenArrays
,
malist
,ExpressionSet
,
tukey.biweight
exDir <- system.file("exData",package="Ringo") exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir) exampleX <- preprocess(exRG) sampleNames(exampleX) <- make.names(paste(exRG$targets$Cy5,"vs",exRG$targets$Cy3,sep="_")) print(exampleX) ### compare VSN to NimbleGen's tukey-biweight scaling exampleX.NG <- preprocess(exRG, method="nimblegen") sampleNames(exampleX.NG) <- sampleNames(exampleX) if (interactive()) corPlot(cbind(exprs(exampleX),exprs(exampleX.NG)), grouping=c("VSN normalized","Tukey-biweight scaled"))