Question: expression set object for metaanalysis
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gravatar for Peevi Ijkl
8.5 years ago by
Peevi Ijkl170
Peevi Ijkl170 wrote:
hello list I know i have been asking the same question over and over again but i just want to make sure am clear. I am loading the CEL files into R using ReadAffy along with the phenodata..then I am performing normalization.Now i want to create another expression set object which I can use for meta-analysis but I am not able to.Any suggestions will be helpful. thanks peevi 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) f1 <- function( x ) ( IQR(x) > 0.5 ) ff <- filterfun(f1) rma_filtered <- genefilter( rma_expression_data, ff ) sum(rma_filtered) rma_data_selected <- rma_expression_data [ rma_filtered, ] dim(rma_expression_data) dim(rma_data_selected) till here I have no errors at all..after this i try the following.. data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,ann otation="hgu133a2") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotatedDataFrameFrom", for signature "ExpressionSet". please help! [[alternative HTML version deleted]]
normalization • 619 views
ADD COMMENTlink modified 8.5 years ago by James W. MacDonald50k • written 8.5 years ago by Peevi Ijkl170
Answer: expression set object for metaanalysis
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gravatar for Kasper Daniel Hansen
8.5 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Your rma_data_selected is already an ExpressionSet (try class(rma_data_selected)), so you already have what you want. Otherwise, your call data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,a nnotation="hgu133a2") should be something like data1<-new("ExpressionSet",exprs=exprs(rma_data_selected),phenoData= phenoData(rma_data_selected),annotation="hgu133a2") (I think it is phenoData and not phenodata, but my memory might fail me) Kasper On Fri, Jan 14, 2011 at 3:51 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > hello list > I know i have been asking the same question over and over again but i just want > to make sure am clear. > I am loading the CEL files into R using ReadAffy along with the phenodata..then > I am performing normalization.Now i want to create another expression set object > > which I can use for meta-analysis but I am not able to.Any suggestions will be > helpful. > thanks > peevi > > 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) > f1 <- function( x ) ( IQR(x) > 0.5 ) > ff <- filterfun(f1) > rma_filtered <- genefilter( rma_expression_data, ff ) > sum(rma_filtered) > rma_data_selected <- rma_expression_data [ rma_filtered, ] > dim(rma_expression_data) > dim(rma_data_selected) > > till here I have no errors at all..after this i try the following.. > > data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,a nnotation="hgu133a2") > > > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "annotatedDataFrameFrom", for > signature "ExpressionSet". > > please help! > > > > > ? ? ? ?[[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 8.5 years ago by Kasper Daniel Hansen6.4k
Answer: expression set object for metaanalysis
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gravatar for James W. MacDonald
8.5 years ago by
United States
James W. MacDonald50k wrote:
Hi Peevi, On 1/14/2011 3:51 PM, Peevi Ijkl wrote: > hello list > I know i have been asking the same question over and over again but i just want > to make sure am clear. Yes you have been asking the same thing over and over. In addition, you have been posting the same question under different subject lines. And you have not responded to requests for your sessionInfo() output, even after it was explained to you in very nice terms what that meant. And you have either not read the posting guide, or have chosen to ignore it. So let me be clear as well. This is a volunteer mailing list where the respondents are choosing to take their time to help answer questions for free. In order to get people to take time to read, understand, and then diagnose your problem, you need to make it easy for that to happen. This is why you were asked for your sessionInfo(). In addition, it is considered bad form to repost the same question over and over, using different subject lines. You may think that will increase the odds that somebody will see your question, but in fact those of us who answer questions see _all_ the questions, and people who abuse the system like that will tend to be ignored. Now the code you post below won't work as written, so you have either made some copy-paste errors, or are simply typing what you think you ran into this email. This isn't helpful. What we need is the actual R session, including the output. Since that can get very long, you should eliminate all steps that are not necessary to show the problem you are having. After you have run the offending code, you also have to run sessionInfo() and add that output to the email. If you have questions about what something like sessionInfo() means, you can always type ?sessionInfo at the R prompt to see the help page. By trying to figure things out on your own and showing that you have done so, people will be more likely to want to help you. Best, Jim > I am loading the CEL files into R using ReadAffy along with the phenodata..then > I am performing normalization.Now i want to create another expression set object > > which I can use for meta-analysis but I am not able to.Any suggestions will be > helpful. > thanks > peevi > > 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) > f1<- function( x ) ( IQR(x)> 0.5 ) > ff<- filterfun(f1) > rma_filtered<- genefilter( rma_expression_data, ff ) > sum(rma_filtered) > rma_data_selected<- rma_expression_data [ rma_filtered, ] > dim(rma_expression_data) > dim(rma_data_selected) > > till here I have no errors at all..after this i try the following.. > > data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,a nnotation="hgu133a2") > > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotatedDataFrameFrom", for > signature "ExpressionSet". > > please help! > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 8.5 years ago by James W. MacDonald50k
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