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Question: Invalid "marrayInfo"
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gravatar for Straubhaar, Juerg
13.7 years ago by
Straubhaar, Juerg300 wrote:
Using the command line: * swirl.samples<-read.marrayInfo(file.path(datadir, "SwirlSample.txt")) directly out of the Vignette: Introduction to the Bioconductor marrayInput packacke, I get the following error: Error in validObject(.Object) : Invalid "marrayInfo" object: Invalid object for slot "maInfo" in class "marrayInfo": got class "NULL", should be or extend class "data.frame" I couldn't parse my sample information into the maInfo object and I noticed it doesn't work with the Bioconductor example file either. Has the marrayInfo Class changed? Juerg Straubhaar, Umass Med [[alternative HTML version deleted]]
ADD COMMENTlink modified 13.7 years ago by Hongxian He20 • written 13.7 years ago by Straubhaar, Juerg300
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gravatar for Jean Yee Hwa Yang
13.7 years ago by
Jean Yee Hwa Yang920 wrote:
Hi Juerg, There is a bug, please download the version marrayClass version 1.2.1 at http://www.bioconductor.org/repository/devel/package/html/marrayClasse s.html Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Thu, 24 Jul 2003, Straubhaar, Juerg wrote: > Using the command line: > > > > * swirl.samples<-read.marrayInfo(file.path(datadir, > "SwirlSample.txt")) > > > > directly out of the Vignette: Introduction to the Bioconductor > marrayInput packacke, I get the following error: > > > > Error in validObject(.Object) : Invalid "marrayInfo" object: Invalid > object for slot "maInfo" in class "marrayInfo": got class "NULL", should > be or extend class "data.frame" > > > > I couldn't parse my sample information into the maInfo object and I > noticed it doesn't work with the Bioconductor example file either. Has > the marrayInfo Class changed? > > > > Juerg Straubhaar, > > Umass Med > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 13.7 years ago by Jean Yee Hwa Yang920
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gravatar for Hongxian He
13.7 years ago by
Hongxian He20
Hongxian He20 wrote:
Hi, Juerg: I just happened to encounter the same problem today. The error lies in the following command in read.marrayInfo(): > descript <- new("marrayInfo", maNotes=notes) Error in validObject(.Object) : Invalid "marrayInfo" object: Invalid object for slot "maInfo" in class "marrayInfo": got class "NULL", should be or extend class "data.frame" The problem is that the constructor of marrayInfo does not allow maInfo slot to be empty. The error disappears if you give the maInfo, e.g. > descript <- new("marrayInfo", maInfo=data.frame(c("trt","ref","ref","trt")), maNotes=notes) Thus for now, you can modify the function to pass in the corresponding maInfo (add maInfo=maInfo to the parameter list, then change the above line to descript <- new("marrayInfo", maInfo=maInfo, maNotes=notes) cheers, Hongxian On Thu, 24 Jul 2003, Straubhaar, Juerg wrote: > Using the command line: > > > > * swirl.samples<-read.marrayInfo(file.path(datadir, > "SwirlSample.txt")) > > > > directly out of the Vignette: Introduction to the Bioconductor > marrayInput packacke, I get the following error: > > > > Error in validObject(.Object) : Invalid "marrayInfo" object: Invalid > object for slot "maInfo" in class "marrayInfo": got class "NULL", should > be or extend class "data.frame" > > > > I couldn't parse my sample information into the maInfo object and I > noticed it doesn't work with the Bioconductor example file either. Has > the marrayInfo Class changed? > > > > Juerg Straubhaar, > > Umass Med > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- Hongxian He Postdoctoral Researcher Center for Bioinformatics University of Pennsylvania
ADD COMMENTlink written 13.7 years ago by Hongxian He20
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