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Kort, Eric ▴ 220
@kort-eric-1483
Last seen 6.1 years ago
United States
Hello. I am running 64 bit R 2.0.1 on SUSE Linux, and despite successful use in the past, I have been recently been unable to normalize some affy data using expresso. I receive an error with list.files that I can not figure out. While list.files seems to generate the error below, if I explicitly call "list.files("./"), I receive no error. Here is my code and the resulting error and traceback: >AB <- ReadAffy(celfile.path="./") > >eset <- expresso(AB, bgcorrect.method="mas", normalize.method="constant", + pmcorrect.method="mas", summary.method="mas", verbose=T) background correction: mas normalization: constant PM/MM correction : mas expression values: mas background correcting...done. normalizing...Error in list.files(path, pattern, all.files, full.names, recursive) : invalid directory argument > > traceback() 7: list.files(...) 6: list.celfiles(celfile.path, full.names = TRUE) 5: AllButCelsForReadAffy(..., filenames = filenames, widget = widget, celfile.path = celfile.path, sampleNames = sampleNames, phenoData = phenoData, description = description) 4: ReadAffy(celfile.path = dir) 3: normalize(afbatch, normalize.method) 2: do.call("normalize", c(alist(afbatch, normalize.method), normalize.param)) 1: expresso(AB, bgcorrect.method = "mas", normalize.method = "constant", pmcorrect.method = "mas", summary.method = "mas", verbose = T) Can someone tell me why this is not working? Thank you, Eric Kort Van Andel Research Institute Grand Rapids, MI 49503 USA This email message, including any attachments, is for the so...{{dropped}}
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@cecilia-mcgregor-1508
Last seen 9.6 years ago
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
On 15 Nov 2005, khan at cshl.edu wrote: > Dear List, > I am using siggenes1.2.17 on R 2.1.1. I have an object of class > "sumSAM". I want to obtain a list of differentially expressed genes, > so I try the following: > sum.sam.out<-summary(sam.out,3.0,ll=FALSE) > When I try to get the list of significant genes > sum.sam.out$row.sig.genes > I get a NULL. > I checked the slotNames(sum.sam.out) > "row.sig.genes" "mat.fdr" "mat.sig" "list.args" > but they are all NULL. How did you check? If sumSAM is an S4 class (which seems to be the case if slotNames gives useful info), then you want to access the contents of the slots using "@" or slot(). For example, sum.sam.out at row.sig.genes HTH, + seth
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Khan, Sohail ▴ 490
@khan-sohail-1137
Last seen 9.6 years ago
Dear List, I am using siggenes1.2.17 on R 2.1.1. I have an object of class "sumSAM". I want to obtain a list of differentially expressed genes, so I try the following: sum.sam.out<-summary(sam.out,3.0,ll=FALSE) When I try to get the list of significant genes sum.sam.out$row.sig.genes I get a NULL. I checked the slotNames(sum.sam.out) "row.sig.genes" "mat.fdr" "mat.sig" "list.args" but they are all NULL. Thanks in advance. -Sohail
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