| 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"))