Question: how to convert a AffyBatch into ExpressionSet object ?
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gravatar for Min Wook Kim
12.3 years ago by
Min Wook Kim20
Min Wook Kim20 wrote:
Dear all, I tried to convert a object of AffyBatch into one of ExpressionSet. but I couldn't get exactly same information between them, actually, The data between original data and the modified data from gcrma was compared. The problem was that the assayData and fetureaData didn't match. Do I have to make new object of AssayData and featuredata by using "new command" ? are there any easy way ? e.g. some function to copy from one to the other. I did it like ; > abatch AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse430_2 (45101 affyids) number of samples=4 number of genes=45101 annotation=mouse4302 notes= > tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) , featureData = featureData(abatch), experimentData = experimentData(abatch), annotation = annotation(abatch), assayData= assayData(abatch)) And what's difference between the following statement and above which were different in assayData defined and exprs ) > tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) , featureData = featureData(abatch), experimentData = experimentData(abatch), annotation = annotation(abatch), exprs = exprs(abatch) ) ------------------------------------------- Finally, I want to make the same structure of the following two objects except the value depending on the effect of gcrma. myRMA was the output of gcrma. Maybe, my trying has a big misunderstanding of them. if do it, please tell me it. > myRMA ExpressionSet (storageMode: lockedEnvironment) assayData: 14707 features, 4 samples element names: exprs phenoData sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b varLabels and varMetadata: sample: arbitrary numbering pheno1: arbitrary numbering featureData rowNames: 1415670_at, 1415671_at, ..., AFFX-TransRecMur/X57349_3_at (14707 total) varLabels and varMetadata: none experimentData: use 'experimentData(object)' Annotation [1] "mouse4302" > tmp ExpressionSet (storageMode: lockedEnvironment) assayData: 1004004 features, 4 samples element names: exprs phenoData sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b varLabels and varMetadata: sample: arbitrary numbering pheno1: arbitrary numbering featureData featureNames: 1, 2, ..., 1004004 (1004004 total) varLabels and varMetadata: none experimentData: use 'experimentData(object)' Annotation [1] "mouse4302" -------------------------------------------------------------------- And additionally, I haven't been able find the picture of description about the hierarchy of classes ; especially Affybatch , EspressionSet and eSet. If to exist, it would be so helpful. > sessionInfo() R version 2.5.1 (2007-06-27) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets" [7] "tcltk" "utils" "methods" "base" other attached packages: mouse4302cdf vsn marray tkWidgets GOstats Category "1.16.0" "2.2.0" "1.14.0" "1.14.0" "2.2.6" "2.2.3" Matrix RBGL graph multtest annaffy KEGG "0.999375-1" "1.12.0" "1.14.2" "1.16.1" "1.8.1" "1.16.1" GO limma affyQCReport geneplotter lattice annotate "1.16.0" "2.10.5" "1.14.0" "1.14.0" "0.15-11" "1.14.1" RColorBrewer affyPLM gcrma matchprobes affydata xtable "1.0-1" "1.12.0" "2.8.1" "1.8.1" "1.11.3" "1.5-1" simpleaffy genefilter survival affy affyio Biobase "2.10.31" "1.14.1" "2.32" "1.14.2" "1.4.1" "1.14.1" DynDoc widgetTools "1.14.0" "1.12.0"
ADD COMMENTlink written 12.3 years ago by Min Wook Kim20
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