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Question: expression set objects
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gravatar for Peevi Ijkl
6.9 years ago by
Peevi Ijkl170
Peevi Ijkl170 wrote:
Hi list.. I am trying to create an expression set object..here is what i did so far.. pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" ) pData(pd) expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) expression_data rma_expression_data <-rma(expression_data) rma_data <- exprs(rma_expression_data) now i want to create an expression set object from the above using the following: ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd, + annotation = "hgu95av2") but I am getting the following error when i use the above Error in validObject(.Object) : invalid class "ExpressionSet" object: 1: row numbers differ for assayData members invalid class "ExpressionSet" object: 2: sample numbers differ for assayData members while if i use rma_expression_data at the highlighted area am getting the following error: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotatedDataFrameFrom", for signature "ExpressionSet" any help would be appreciated. thanks peevi [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.9 years ago by Vincent J. Carey, Jr.6.2k • written 6.9 years ago by Peevi Ijkl170
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gravatar for Vincent J. Carey, Jr.
6.9 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
what is your sessionInfo() result? On Thu, Jan 13, 2011 at 10:58 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > Hi list.. > I am trying to create an expression set object..here is what i did so far.. > > pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" ) > pData(pd) > expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) > expression_data > rma_expression_data <-rma(expression_data) > rma_data <- exprs(rma_expression_data) > > now i want to create an expression set object from the above using the > following: > ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd, > + annotation = "hgu95av2") > but I am getting the following error when i use the above > > Error in validObject(.Object) : > ?invalid class "ExpressionSet" object: 1: row numbers differ for assayData > members > invalid class "ExpressionSet" object: 2: sample numbers differ for assayData > members > > while if i use rma_expression_data at the highlighted area am getting the > following error: > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "annotatedDataFrameFrom", for > signature "ExpressionSet" > > any help would be appreciated. > > thanks > peevi > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 6.9 years ago by Vincent J. Carey, Jr.6.2k
Am sorry I dont understand your question ________________________________ From: Vincent Carey <stvjc@channing.harvard.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Fri, January 14, 2011 2:34:41 AM Subject: Re: [BioC] expression set objects what is your sessionInfo() result? > Hi list.. > I am trying to create an expression set object..here is what i did so far.. > > pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" ) > pData(pd) > expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) > expression_data > rma_expression_data <-rma(expression_data) > rma_data <- exprs(rma_expression_data) > > now i want to create an expression set object from the above using the > following: > ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd, > + annotation = "hgu95av2") > but I am getting the following error when i use the above > > Error in validObject(.Object) : > invalid class "ExpressionSet" object: 1: row numbers differ for assayData > members > invalid class "ExpressionSet" object: 2: sample numbers differ for assayData > members > > while if i use rma_expression_data at the highlighted area am getting the > following error: > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotatedDataFrameFrom", for > signature "ExpressionSet" > > any help would be appreciated. > > thanks > peevi > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.9 years ago by Peevi Ijkl170
On Fri, Jan 14, 2011 at 11:10 AM, Peevi Ijkl <ipeevi@yahoo.com> wrote: > > > Am sorry I dont understand your question > > Hi, Peevi. Please READ the posting guide here: http://www.bioconductor.org/help/mailing-list/posting-guide/ sessionInfo() is an R function. When you are writing to the list, as per the posting guide, you must include the output of sessionInfo() and, when reporting an error, the output of traceback(). Sean > > ________________________________ > From: Vincent Carey <stvjc@channing.harvard.edu> > > Cc: bioconductor@stat.math.ethz.ch > Sent: Fri, January 14, 2011 2:34:41 AM > Subject: Re: [BioC] expression set objects > > what is your sessionInfo() result? > > > > Hi list.. > > I am trying to create an expression set object..here is what i did so > far.. > > > > pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, > sep=";" ) > > pData(pd) > > expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) > > expression_data > > rma_expression_data <-rma(expression_data) > > rma_data <- exprs(rma_expression_data) > > > > now i want to create an expression set object from the above using the > > following: > > ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd, > > + annotation = "hgu95av2") > > but I am getting the following error when i use the above > > > > Error in validObject(.Object) : > > invalid class "ExpressionSet" object: 1: row numbers differ for > assayData > > members > > invalid class "ExpressionSet" object: 2: sample numbers differ for > assayData > > members > > > > while if i use rma_expression_data at the highlighted area am getting the > > following error: > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function > "annotatedDataFrameFrom", for > > signature "ExpressionSet" > > > > any help would be appreciated. > > > > thanks > > peevi > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.9 years ago by Sean Davis21k
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