Question: Problems with gcrma using latest version of R and Bioconductor
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gravatar for Sebastian Bauer
12.4 years ago by
Sebastian Bauer60 wrote:
Hello, I have some problems with the gcrma normalization procedure. Please look at the output: ---- > Chips.norm<-gcrma(Chips.raw) Adjusting for optical effect............................Done. Computing affinities.Error in get(x, envir, mode, inherits) : variable "mouse4302dim" was not found > traceback() 9: get(nam) 8: get("NROW", get(nam)) 7: xy2indices(p$x, p$y, cdf = cdfpackagename) 6: inherits(x, "factor") 5: is.factor(x) 4: match(xy2indices(p$x, p$y, cdf = cdfpackagename), pmIndex) 3: compute.affinities(cdfName(object), verbose = verbose) 2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source, NCprobe = NCprobe, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, optical.correct = optical.correct, verbose = verbose, fast = fast) 1: gcrma(Chips.raw) ---- I'm using R Version 2.5.1 and Bioconductor 2.0. I've reinstalled all needed packages, but I noticed no difference in the behavior. The same procedure worked with previous versions of R and Bioconductor though. It's possible to circumvent the problem? On reply, please CC me as I'm not subscribed to the list. Thanks in advance! Bye, Sebastian
normalization cdf gcrma • 555 views
ADD COMMENTlink modified 12.4 years ago by James W. MacDonald52k • written 12.4 years ago by Sebastian Bauer60
Answer: Problems with gcrma using latest version of R and Bioconductor
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gravatar for James W. MacDonald
12.4 years ago by
United States
James W. MacDonald52k wrote:
Hi Sebastian, Please always give us the output of sessionInfo() as well. Just telling us you have BioC 2.0 isn't sufficient. For instance, I get this to work: > dat <- ReadAffy(filenames=list.celfiles()[1:5]) > eset <- gcrma(dat) Adjusting for optical effect.....Done. Computing affinities.Done. Adjusting for non-specific binding.....Done. Normalizing Calculating Expression > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 45101 features, 5 samples element names: exprs phenoData rowNames: Kretzler 730.CEL, Kretzler 731.CEL, ..., Kretzler 734.CEL (5 total) varLabels and varMetadata: sample: arbitrary numbering featureData featureNames: 1415670_at, 1415671_at, ..., AFFX-TrpnX-M_at (45101 total) varLabels and varMetadata: none experimentData: use 'experimentData(object)' Annotation [1] "mouse4302" > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" [7] "utils" "methods" "base" other attached packages: mouse4302probe mouse4302cdf gcrma matchprobes affy "1.16.0" "1.16.0" "2.8.1" "1.8.1" "1.14.2" affyio Biobase rcompgen "1.4.1" "1.14.0" "0.1-13" Sebastian Bauer wrote: > Hello, > > I have some problems with the gcrma normalization procedure. Please look > at the output: > > ---- > > > > Chips.norm<-gcrma(Chips.raw) > Adjusting for optical effect............................Done. > Computing affinities.Error in get(x, envir, mode, inherits) : variable > "mouse4302dim" was not found > > traceback() > 9: get(nam) > 8: get("NROW", get(nam)) > 7: xy2indices(p$x, p$y, cdf = cdfpackagename) > 6: inherits(x, "factor") > 5: is.factor(x) > 4: match(xy2indices(p$x, p$y, cdf = cdfpackagename), pmIndex) > 3: compute.affinities(cdfName(object), verbose = verbose) > 2: bg.adjust.gcrma(object, affinity.info = affinity.info, > affinity.source = affinity.source, > NCprobe = NCprobe, type = type, k = k, stretch = stretch, > correction = correction, GSB.adjust = GSB.adjust, rho = rho, > optical.correct = optical.correct, verbose = verbose, fast = fast) > 1: gcrma(Chips.raw) > > ---- > > I'm using R Version 2.5.1 and Bioconductor 2.0. I've reinstalled all > needed packages, but I noticed no difference in the behavior. The same > procedure worked with previous versions of R and Bioconductor though. > It's possible to circumvent the problem? > > On reply, please CC me as I'm not subscribed to the list. > > Thanks in advance! > > Bye, > Sebastian > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 12.4 years ago by James W. MacDonald52k
Hi James, James W. MacDonald wrote: > Please always give us the output of sessionInfo() as well. Just telling > us you have BioC 2.0 isn't sufficient. For instance, I get this to work: Thanks for your quick reply. You sessionInfo() output gave me the hint that I did not update some of the annotation packages whose existence I wasn't aware of (initially, I updated only the mouse4302 package) :) After updating the rest, all seems to work again. However, from an user's point of view, I would rather like to see an appropriate error message coming up which complains about non-matching versions of the required package. Is there such a mechanism in Bioconductor/R? Ciao, Sebastian
ADD REPLYlink written 12.4 years ago by Sebastian Bauer60
Hi Sebastian, I don't know if there is a method to check for mis-matched packages, but there is a simple way to update your packages so in truth there should be no need for such checking. If you update your R version, all you need to do is then install all needed packages using biocLite(). If for whatever reason you haven't used biocLite() to install the packages, you can always use update.packages(): biocLite("Biobase") ##ensure Biobase is correct version library(Biobase) repos <- biocReposList() update.packages(repos=repos, ask=FALSE) If you follow either prescription then you should never have to worry about mis-matched packages. If you do something else, then you are on your own ;-D Best, Jim Sebastian Bauer wrote: > Hi James, > > James W. MacDonald wrote: >> Please always give us the output of sessionInfo() as well. Just >> telling us you have BioC 2.0 isn't sufficient. For instance, I get >> this to work: > > Thanks for your quick reply. You sessionInfo() output gave me the hint > that I did not update some of the annotation packages whose existence I > wasn't aware of (initially, I updated only the mouse4302 package) :) > After updating the rest, all seems to work again. > > However, from an user's point of view, I would rather like to see an > appropriate error message coming up which complains about non- matching > versions of the required package. Is there such a mechanism in > Bioconductor/R? > > Ciao, > Sebastian -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 12.4 years ago by James W. MacDonald52k
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