Question: expression set object
0
gravatar for Peevi Ijkl
8.8 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 • 408 views
ADD COMMENTlink modified 8.8 years ago by Sean Davis21k • written 8.8 years ago by Peevi Ijkl170
Answer: expression set object
0
gravatar for Sean Davis
8.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Fri, Jan 14, 2011 at 3:26 PM, Peevi Ijkl <ipeevi@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") > Hi, Peevi. "pData" in the above line is not a variable that you defined in the code above. If it was defined elsewhere, it is a bad choice of variable names because there is a method called pData. If it was not defined by you, that is probably the problem and you want to use "pd" instead of "pData". You still NEED to provide the output of sessionInfo() for EVERY email at least once and NEED to provide the output of traceback() for every error message. Sean > > 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@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 COMMENTlink written 8.8 years ago by Sean Davis21k
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