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...BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces at stat.math.ethz.ch on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($File...

...4,5,6,7,8,9") # Initialize exprSet object pD <- new("phenoData", pData=pd, varLabels=pdN); # This is my eSet!!! metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), phenoData=pD) I get the following error: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Can someone suggest me how to use the new method AnnotatedDataFrame to create eSet? Thanks Manisha [[alternative HTML version deleted]]

...ot;, row.names = TRUE, > col.names = TRUE) > testFile [1] "C:\\DOCUME~1\\Jaswanth\\LOCALS~1\\Temp\\RtmpXrUE8T\\file2ea6bb3" > eSet <- read.exprSet(testFile) Warning messages: 1: read.exprSet is deprecated, use readExpresionSet instead 2: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 4: The exprSet class is deprecated, use ExpressionSet instead 5: The exprSet class is deprecated, use ExpressionSet instead 6: The exprSet class is deprecated, use ExpressionSet instead 7: The ex...

...es.com/1.png http://clarezoe.googlepages.com/2.png http://clarezoe.googlepages.com/3.png ------------- Errors also show in the terminal as below, ------------- > Error: no function to return from, jumping to top level In addition: Warning messages: 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Error in exprs(RawAffyData) : no function to return from, jumping to top level -------------- I'm running R version 2.6.1 under Linux Ubuntu 7.10 -------------- My sessionInfo is shown...

...; .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots > .. .. .. .. ..@ .Data:List of 1 > .. .. .. .. .. ..$ : int [1:3] 1 0 0 > ..@ assayData :<environment: 0x1078636e8> > ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots > .. .. ..@ varMetadata :'data.frame': 21 obs. of 1 variable: > .. .. .. ..$ labelDescription: chr [1:21] " Patient ID" " Date of diagnosis" " Gender of the patient" " Age of the patient at e...

...tes() to probe inside the object, and something@something$something to walk it and explore. Is there any other way? Also, without reading documentations, is there a way to know what functions are available to extract data from it? For example, there is sampleNames() which works on ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How do I know they are available (as sometimes I can't recall where I've seen them and I forgot the function names). And what are R functions? Are those two separate functions or polymorphic functions? I'm also pretty confused about S3, S4, or the re...

Every now and then I realize that my attempts to document what all dataframes consist of are unsufficient. So far, I have been writing notes in an external file. Are there any better ways to do this within R? One possibility could be to set up the data as packages, but I would like to have a solution on a lower level, closer to data. I can't find any pointers in the standard manuals.

...ethods > > ### ** Examples > > library(yeastRNASeq) > data(geneLevelData) > data(yeastGC) > > sub <- intersect(rownames(geneLevelData), names(yeastGC)) > > mat <- as.matrix(geneLevelData[sub,]) > > data <- newSeqExpressionSet(mat, + phenoData=AnnotatedDataFrame( + data.frame(conditions=factor(c("mut", "mut", "wt", "wt")), + row.names=colnames(geneLevelData))), + featureData=AnnotatedDataFrame(data.frame(gc=yeastGC[sub]))) > > MDPlot(data,c(1,3...

...cel 2 E-CBIL-28-raw-cel-1435145167.cel 2 E-CBIL-28-raw-cel-1435145387.cel 3 E-CBIL-28-raw-cel-1435145099.cel 3 (I'm not sure why the disease column isn't showing up as a tab here, but it is sep by "\t" in my file. I've tried several variations on these: pd <- read.AnnotatedDataFrame ("new_treat.txt" , header = TRUE , sep="\t", row.names = "SampleID", colClasses = c(Disease = "character")) And I keep on getting this error: Error in read.table(filename, sep = sep, header = header, quote = quote, : more columns than column names An...

...quot; [5] "AD_Ctrl_6.CEL" "AD_Traite_10.CEL" "AD_Traite_11.CEL" "AD_Traite_7.CEL" [9] "AD_Traite_8.CEL" "AD_Traite_9.CEL" > test <- read.celfiles(cel.files) Platform design info loaded. > phenoData(test) <- read.AnnotatedDataFrame("phenoData.txt", header = TRUE, row.name=1) > class(test) [1] "GeneFeatureSet" attr(,"package") [1] "oligoClasses" > class(phenoData) [1] "standardGeneric" attr(,"package") [1] "methods" > eset <- rma(test)...

...le: Name FileName Target 0h1 GSM286031.CEL control 0h2 GSM286032.CEL control 0h3 GSM286033.CEL control 3h1 GSM286034.CEL three 3h2 GSM286035.CEL three 3h3 GSM286036.CEL three 6h1 GSM286037.CEL six 6h2 GSM286038.CEL six 6h3 GSM286039.CEL six library(affy) library(limma) library(vsn) pd <- read.AnnotatedDataFrame("er_for_affy.txt", header = TRUE, row.names = 2) pData(pd) #### load a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmco...

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...;myphenotypicdatacheck.txt",sep="\t",col.names=NA) rownames(myphenotypicdata) colnames(myphenotypicdata) #[1] "species" "time" summary(myphenotypicdata) all(rownames(myphenotypicdata)==colnames(myexprdata)) #[1] TRUE #Create annotated Data Frame adf<-new("AnnotatedDataFrame",data=phenotypicdata) #dim means: dimension of an object. dim(adf) #rowNames columnNames # 28 2 rownames(adf) #NULL #read in galfile readGAL("Galfile.gal") #Create eset object eSet<-new("ExpressionSet",exprs=myexprdata,phenoData=adf,annotation="Galf...

Hi, I agree with Henrik that his suggestion to have "dimension vector attributes" working like dimnames (see below) would be an extremely useful infrastructure adittion to R. If this is not considered for R-core, I am happy to try to implement this in a package, as a new class. And possibly do the same thing for data frames. Should you have any comments, ideas or suggestions about it,