Displaying 3 results from an estimated 3 matches for "bgcorrect".
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_bgcorrect
2007 Dec 24
3
Affy Package
Dear R Users,
In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best:
bgcorrect.metod = rma rma2 mas
normalize.method = qspline quantiles loess
pmcorrect.method = pmonly subtractmm mas
summary.method = liwong avgdiff medianpolish mas
There are many options within each method. I would appreciate a hint on the best combination.
Thank you very much in advance.
Roger
Roger...
2007 Aug 06
1
Problems with expresso
...a-spikein data from
affycompII. But there is an error:
> library(affy)
> path <- "z:/Microarray/hgu133a-spikein/rawdata"
> celFile <- list.celfiles(path=path,full.names=TRUE);
> affyBatch <- ReadAffy(filenames=celFile[1:6]);
> eset1 <-
expresso(affyBatch,bgcorrect.method="rma",normalize.method="quantiles",summary.method="medianpolish")
background correction: rma
normalization: quantiles
PM/MM correction :
expression values: medianpolish
background correcting...done.
normalizing...done.
Fehler in function (classes, fdef, mtable)...
2003 Sep 02
0
File in use error (PR#4047)
...y(affy)")
sPath = "c:\\temp\\"
x.EvaluateNoReturn("setwd(" + Chr(34) + sPath + Chr(34) + ")")
'Reading files...
x.EvaluateNoReturn("data <- ReadAffy()")
'Calculating RMA expression values...
x.EvaluateNoReturn("eset <- expresso(data, bgcorrect.method=" + Chr(34) + "rma"
+ Chr(34) + ", normalize.method=" + Chr(34) + "quantiles" + Chr(34) + ",
pmcorrect.method=" + Chr(34) + "pmonly" + Chr(34) + ", summary.method=" +
Chr(34) + "avgdiff" + Chr(34) + ")")
...