Question: error coercing an exprSet to ExpressionSet
0
gravatar for Kimpel, Mark W
13.1 years ago by
Kimpel, Mark W890 wrote:
I have encountered an error when attempting to coerce an exprSet to an ExpressionSet. Below is my code, output, and sessionInfo(). What is the problem? Thanks, Mark >isCurrent(eset, "exprSet") R Biobase annotatedDataset exprSet TRUE TRUE TRUE TRUE > > as(exprSet=eset,"ExpressionSet") Error in as(exprSet = eset, "ExpressionSet") : unused argument(s) (exprSet = <s4 object="" of="" class="" "exprset"="">) > sessionInfo() R version 2.4.0 (2006-10-03) 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" "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" other attached packages: rgu34acdf svMisc multtest affycoretools biomaRt RCurl XML GOstats Category genefilter survival "1.14.0" "0.9-5" "1.12.0" "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.3" "2.0.3" "1.12.0" "2.29" KEGG RBGL annotate GO graph RankProd RWinEdt limma affy affyio Biobase "1.14.1" "1.10.0" "1.12.0" "1.14.1" "1.12.0" "2.6.0" "1.7-5" "2.9.1" "1.12.1" "1.2.0" "1.12.2" > Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Work, & Mobile ? (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX
ADD COMMENTlink modified 13.1 years ago by Seth Falcon7.4k • written 13.1 years ago by Kimpel, Mark W890
Answer: error coercing an exprSet to ExpressionSet
0
gravatar for Seth Falcon
13.1 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I have encountered an error when attempting to coerce an exprSet to an > ExpressionSet. Below is my code, output, and sessionInfo(). What is > the problem? Thanks, Mark > >>isCurrent(eset, "exprSet") > R Biobase annotatedDataset exprSet TRUE TRUE TRUE TRUE >> as(exprSet=eset,"ExpressionSet") > Error in as(exprSet = eset, "ExpressionSet") : unused argument(s) > (exprSet = <s4 object="" of="" class="" "exprset"="">) Can you try again without naming the argument? Like this: ans <- as(eset, "ExpressionSet") The error message is telling you that 'exprSet' is not one of the formal arguments to the as function. You can see those arguments using the args() function: > args(as) function (object, Class, strict = TRUE, ext = possibleExtends(thisClass, Class)) So if you wanted, you could call as(object=eset, Class="ExpressionSet"). Hope that gets you going again. + seth
ADD COMMENTlink written 13.1 years ago by Seth Falcon7.4k
Seth, Didn't work, here's what I got for output: as(eset,"ExpressionSet") Error in validObject(.Object) : invalid class "ExpressionSet" object: featureNames differ between AssayData members Enter a frame number, or 0 to exit 1: as(eset, "ExpressionSet") 2: asMethod(object) 3: new("ExpressionSet", phenoData = as(phenoData(from), "AnnotatedDataFrame"), experimentData = desc, annotation = annotation(from), exprs = exprs, se.exp 4: initialize(value, ...) 5: initialize(value, ...) 6: .local(.Object, ...) 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotati 8: eval(call, callEnv) 9: eval(expr, envir, enclos) 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 11: .local(.Object, ...) 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotati 13: eval(call, callEnv) 14: eval(expr, envir, enclos) 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 16: .local(.Object, ...) 17: callNextMethod(.Object, ...) 18: eval(call, callEnv) 19: eval(expr, envir, enclos) 20: .nextMethod(.Object, ...) 21: validObject(.Object) Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: Thursday, November 16, 2006 8:18 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] error coercing an exprSet to ExpressionSet Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I have encountered an error when attempting to coerce an exprSet to an > ExpressionSet. Below is my code, output, and sessionInfo(). What is > the problem? Thanks, Mark > >>isCurrent(eset, "exprSet") > R Biobase annotatedDataset exprSet TRUE TRUE TRUE TRUE >> as(exprSet=eset,"ExpressionSet") > Error in as(exprSet = eset, "ExpressionSet") : unused argument(s) > (exprSet = <s4 object="" of="" class="" "exprset"="">) Can you try again without naming the argument? Like this: ans <- as(eset, "ExpressionSet") The error message is telling you that 'exprSet' is not one of the formal arguments to the as function. You can see those arguments using the args() function: > args(as) function (object, Class, strict = TRUE, ext = possibleExtends(thisClass, Class)) So if you wanted, you could call as(object=eset, Class="ExpressionSet"). Hope that gets you going again. + seth _______________________________________________ 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
ADD REPLYlink written 13.1 years ago by Kimpel, Mark W890
Answer: error coercing an exprSet to ExpressionSet
0
gravatar for Seth Falcon
13.1 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Seth, > > Didn't work, here's what I got for output: > > as(eset,"ExpressionSet") > Error in validObject(.Object) : invalid class "ExpressionSet" object: > featureNames differ between AssayData members Here's my guess of what's going on. Does your exprSet, eset, have data in both the exprs and se.exprs slot? I suspect that the answer is yes and that the rownames of these two matrices do not match (this is what the error is telling us). So I would compare rownames(se.exprs(eset)) with rownames(exprs(eset)) and make them match. Then try the convert again. + seth
ADD COMMENTlink written 13.1 years ago by Seth Falcon7.4k
Seth, You are correct. justRMA is not giving rownames to the se.exprs slot. Below is the nice output I got after following your advice. At some point in the future will justRMA and other background correction/normalization routines in Affy be outputting ExpressionSet rather than the deprecated exprSet? > rownames(se.exprs(eset) + ) NULL > > rownames(se.exprs(eset))<-rownames(exprs(eset)) > > as(eset,"ExpressionSet") ExpressionSet (storageMode: lockedEnvironment) assayData: 8799 features, 59 samples element names: exprs, se.exprs phenoData sampleNames: WS02R111.CEL, WS02R112.CEL, ..., WS02R526.CEL (59 total) varLabels and varMetadata: sampleNames: read from file Strain: read from file Region: read from file Animal: read from file featureData featureNames: A01157cds_s_at, A03913cds_s_at, ..., Z96106_at (8799 total) varLabels and varMetadata: none experimentData: use 'experimentData(object)' Annotation [1] "rgu34a" Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: Thursday, November 16, 2006 10:41 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] error coercing an exprSet to ExpressionSet "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Seth, > > Didn't work, here's what I got for output: > > as(eset,"ExpressionSet") > Error in validObject(.Object) : invalid class "ExpressionSet" object: > featureNames differ between AssayData members Here's my guess of what's going on. Does your exprSet, eset, have data in both the exprs and se.exprs slot? I suspect that the answer is yes and that the rownames of these two matrices do not match (this is what the error is telling us). So I would compare rownames(se.exprs(eset)) with rownames(exprs(eset)) and make them match. Then try the convert again. + seth _______________________________________________ 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
ADD REPLYlink written 13.1 years ago by Kimpel, Mark W890
Answer: error coercing an exprSet to ExpressionSet
0
gravatar for Seth Falcon
13.1 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Seth, > > You are correct. justRMA is not giving rownames to the se.exprs slot. > Below is the nice output I got after following your advice. Victory! That justRMA doesn't give proper row names to se.exprs is a bug. We'll fix it. > At some point in the future will justRMA and other background > correction/normalization routines in Affy be outputting ExpressionSet > rather than the deprecated exprSet? Yes, the plan is that in the next release all functions that currently produce exprSets will instead produce ExpressionSet objects. + seth
ADD COMMENTlink written 13.1 years ago by Seth Falcon7.4k
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