search for: pmcorrect

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 L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department o...

...kage: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. registering new summary method 'pdnn'. registering new pmcorrect method 'pdnn' and 'pdnnpredict'. > library(hgu133atagprobe) Loading required package: AnnotationDbi > energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u133a.txt", package = "affypdnn") > params.chiptype <- pdnn.params.c...

...Frame("er_for_affy.txt", header = TRUE, row.names = 2) pData(pd) #### load a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = "medianpolish") ### genes with highest variation library(hgu133plus2.db) rsd <- apply(exprs(x), 1, sd) sel <- order(rsd, decreasing = TRUE)[1:250] u<-mget(row.names(exprs(x)[sel,]),hgu133plus2SYMBOL) heatmap(exprs(x)[sel, ], labRow=...

.... 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) + ")") 'Writng output data x.EvaluateNoReturn("write.exprs(eset,file=" + Chr(34) + "output.txt" + Chr(34) + ")") x.Close() --...

...ric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some sort of memory error that crashes the R program. Specifically it states: R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3) R(1763) malloc: *** error: can't allocate region R(1763) malloc: *** set a...