Problems with gcrma using latest version of R and Bioconductor

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Sebastian Bauer ▴ 60

@sebastian-bauer-2067

Last seen 9.6 years ago

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 Normalization cdf gcrma • 904 views

ADD COMMENT • link updated 16.8 years ago by James W. MacDonald 65k • written 16.8 years ago by Sebastian Bauer ▴ 60

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 2 hours ago

United States

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 COMMENT • link 16.8 years ago James W. MacDonald 65k

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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 REPLY • link 16.8 years ago Sebastian Bauer ▴ 60

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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 REPLY • link 16.8 years ago James W. MacDonald 65k

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