ExpressionSet, fitPLM confusion
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Georg Otto ▴ 510
@georg-otto-956
Last seen 8.3 years ago
Dear Bioconductors, Once more, I am a bit confused about an error linked with the new ExpressionSet class. What I am trying to do is to apply fitPLM to an AffyBatch object. First, I generate the AffyBatch object like this: targets<-new("AnnotatedDataFrame") pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) Data<-ReadAffy(celfile.path =cel.path, filenames = sampleNames(targets), verbose=TRUE) Then I use fitPLM and get an error: Pset<-fitPLM(Data) Error in .Deprecated(msg = EXPRSET_DEPR_MSG) : unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead") However ?fitPLM tells me: This function converts an 'AffyBatch' into an 'PLMset' by fitting a specified robust linear model to the probe level data And class() confirms that my object is indeed an AffyBatch: class(Data) [1] "AffyBatch" attr(,"package") [1] "affy" I think I am working with the last versions of the needed libraries (see below). They were updated from the devel repository from source. Any hints? Best, Georg sessionInfo() R version 2.4.0 (2006-10-03) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: zebrafishcdf affyPLM gcrma matchprobes affydata affy "1.15.0" "1.11.8" "2.7.1" "1.7.1" "1.11.1" "1.13.12" affyio Biobase "1.3.1" "1.13.28"
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio • 1.2k views
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@wolfgang-huber-3550
Last seen 11 weeks ago
EMBL European Molecular Biology Laborat…
Dear Georg, to use the devel versions of Bioconductor (ie what will be Bioconductor 2.0) you will need to use a more recent version of R (what will be R 2.5): the new code in Biobase uses an argument "msg" of the .Deprecated function that was not yet there in R 2.4. See http://www.bioconductor.org/download/BioC2.0/ "BioC 2.0 is currently in development. It is being designed to work with R 2.5.z and is expected to be released in April of 2007." Best wishes Wolfgang Otto wrote: > Dear Bioconductors, > > Once more, I am a bit confused about an error linked with the new > ExpressionSet class. What I am trying to do is to apply fitPLM to an > AffyBatch object. First, I generate the AffyBatch object like this: > > targets<-new("AnnotatedDataFrame") > pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) > > > Data<-ReadAffy(celfile.path =cel.path, > filenames = sampleNames(targets), > verbose=TRUE) > > > Then I use fitPLM and get an error: > > Pset<-fitPLM(Data) > > Error in .Deprecated(msg = EXPRSET_DEPR_MSG) : > unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead") > > However ?fitPLM tells me: > > This function converts an 'AffyBatch' into an 'PLMset' by fitting a > specified robust linear model to the probe level data > > And class() confirms that my object is indeed an AffyBatch: > > class(Data) > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > > I think I am working with the last versions of the needed libraries > (see below). They were updated from the devel repository from > source. Any hints? > > Best, > > Georg > > > sessionInfo() > > R version 2.4.0 (2006-10-03) > x86_64-redhat-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > zebrafishcdf affyPLM gcrma matchprobes affydata affy > "1.15.0" "1.11.8" "2.7.1" "1.7.1" "1.11.1" "1.13.12" > affyio Biobase > "1.3.1" "1.13.28" > > _______________________________________________ > 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 -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Hi Georg, In addition to what Wolfgang told you, the affyPLM package in the devel repository won't work with R-2.5.0 yet, because some of the changes that have been made to the ExpressionSet object have not been addressed in the affyPLM package. > dat <- ReadAffy() > pset <- fitPLM(dat) Error in checkSlotAssignment(object, name, value) : assignment of an object of class "AnnotatedDataFrame" is not valid for slot "phenoData" in an object of class "PLMset"; is(value, "phenoData") is not TRUE In addition: Warning message: The exprSet class is deprecated, use ExpressionSet instead Your best bet at this time is to go back to using release versions. Best, Jim Wolfgang Huber wrote: > > Dear Georg, > > to use the devel versions of Bioconductor (ie what will be Bioconductor > 2.0) you will need to use a more recent version of R (what will be R > 2.5): the new code in Biobase uses an argument "msg" of the .Deprecated > function that was not yet there in R 2.4. > > See http://www.bioconductor.org/download/BioC2.0/ > "BioC 2.0 is currently in development. It is being designed to work with > R 2.5.z and is expected to be released in April of 2007." > > Best wishes > Wolfgang > > Otto wrote: > >>Dear Bioconductors, >> >>Once more, I am a bit confused about an error linked with the new >>ExpressionSet class. What I am trying to do is to apply fitPLM to an >>AffyBatch object. First, I generate the AffyBatch object like this: >> >>targets<-new("AnnotatedDataFrame") >>pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) >> >> >>Data<-ReadAffy(celfile.path =cel.path, >> filenames = sampleNames(targets), >> verbose=TRUE) >> >> >>Then I use fitPLM and get an error: >> >>Pset<-fitPLM(Data) >> >>Error in .Deprecated(msg = EXPRSET_DEPR_MSG) : >> unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead") >> >>However ?fitPLM tells me: >> >>This function converts an 'AffyBatch' into an 'PLMset' by fitting a >>specified robust linear model to the probe level data >> >>And class() confirms that my object is indeed an AffyBatch: >> >>class(Data) >>[1] "AffyBatch" >>attr(,"package") >>[1] "affy" >> >> >>I think I am working with the last versions of the needed libraries >>(see below). They were updated from the devel repository from >>source. Any hints? >> >>Best, >> >>Georg >> >> >>sessionInfo() >> >>R version 2.4.0 (2006-10-03) >>x86_64-redhat-linux-gnu >> >>locale: >>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C >> >>attached base packages: >>[1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>[7] "datasets" "methods" "base" >> >>other attached packages: >>zebrafishcdf affyPLM gcrma matchprobes affydata affy >> "1.15.0" "1.11.8" "2.7.1" "1.7.1" "1.11.1" "1.13.12" >> affyio Biobase >> "1.3.1" "1.13.28" >> >>_______________________________________________ >>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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Hi, maybe a workaround would be to have a copy of the new version of .Deprecated() in the global environment. Here it is: .Deprecated <- function (new, package = NULL, msg) { if (missing(msg)) { msg <- gettextf("'%s' is deprecated.\n", as.character(sys.call(sys.parent())[[1]])) if (!missing(new)) msg <- c(msg, gettextf("Use '%s' instead.\n", new)) msg <- c(msg, if (!is.null(package)) gettextf("See help(\"Deprecated\") and help(\"%s-deprecated\").", package) else gettext("See help(\"Deprecated\")")) } else msg = as.character(msg) warning(paste(msg, collapse = ""), call. = FALSE, domain = NA) } If you don't bother with the 'msg' you could even do: .Deprecated <- function(..., msg) base::.Deprecated(...) I haven't tried it with your example, though. /Henrik On 12/15/06, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Georg, > > In addition to what Wolfgang told you, the affyPLM package in the devel > repository won't work with R-2.5.0 yet, because some of the changes that > have been made to the ExpressionSet object have not been addressed in > the affyPLM package. > > > dat <- ReadAffy() > > pset <- fitPLM(dat) > Error in checkSlotAssignment(object, name, value) : > assignment of an object of class "AnnotatedDataFrame" is not valid for > slot "phenoData" in an object of class "PLMset"; is(value, "phenoData") > is not TRUE > In addition: Warning message: > The exprSet class is deprecated, use ExpressionSet instead > > Your best bet at this time is to go back to using release versions. > > Best, > > Jim > > > Wolfgang Huber wrote: > > > > Dear Georg, > > > > to use the devel versions of Bioconductor (ie what will be Bioconductor > > 2.0) you will need to use a more recent version of R (what will be R > > 2.5): the new code in Biobase uses an argument "msg" of the .Deprecated > > function that was not yet there in R 2.4. > > > > See http://www.bioconductor.org/download/BioC2.0/ > > "BioC 2.0 is currently in development. It is being designed to work with > > R 2.5.z and is expected to be released in April of 2007." > > > > Best wishes > > Wolfgang > > > > Otto wrote: > > > >>Dear Bioconductors, > >> > >>Once more, I am a bit confused about an error linked with the new > >>ExpressionSet class. What I am trying to do is to apply fitPLM to an > >>AffyBatch object. First, I generate the AffyBatch object like this: > >> > >>targets<-new("AnnotatedDataFrame") > >>pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) > >> > >> > >>Data<-ReadAffy(celfile.path =cel.path, > >> filenames = sampleNames(targets), > >> verbose=TRUE) > >> > >> > >>Then I use fitPLM and get an error: > >> > >>Pset<-fitPLM(Data) > >> > >>Error in .Deprecated(msg = EXPRSET_DEPR_MSG) : > >> unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead") > >> > >>However ?fitPLM tells me: > >> > >>This function converts an 'AffyBatch' into an 'PLMset' by fitting a > >>specified robust linear model to the probe level data > >> > >>And class() confirms that my object is indeed an AffyBatch: > >> > >>class(Data) > >>[1] "AffyBatch" > >>attr(,"package") > >>[1] "affy" > >> > >> > >>I think I am working with the last versions of the needed libraries > >>(see below). They were updated from the devel repository from > >>source. Any hints? > >> > >>Best, > >> > >>Georg > >> > >> > >>sessionInfo() > >> > >>R version 2.4.0 (2006-10-03) > >>x86_64-redhat-linux-gnu > >> > >>locale: > >>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C > >> > >>attached base packages: > >>[1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > >>[7] "datasets" "methods" "base" > >> > >>other attached packages: > >>zebrafishcdf affyPLM gcrma matchprobes affydata affy > >> "1.15.0" "1.11.8" "2.7.1" "1.7.1" "1.11.1" "1.13.12" > >> affyio Biobase > >> "1.3.1" "1.13.28" > >> > >>_______________________________________________ > >>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 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > 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 >
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