Hi Min Wook, The discrepancy is because you are comparing the probe-level data from an AffyBatch object to the probeset-level data of an ExpressionSet created by gcrma(). Why would you want to convert an AffyBatch object directly into an ExpressionSet object without summarizing the probe-level data into probeset data? The AffyBatch object extends the ExpressionSet structure specifically for probe-level data (individual PM and MM intensities), and typically ExpressionSet objects are reserved for summarized probeset data. For more details on the data classes, use ?"AffyBatch" and ?"ExpressionSet". Cheers, Jenny At 11:42 AM 8/22/2007, Min Wook Kim 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_U S.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" > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Hi Jenny, thanks a lot. I know the relationship between AffyBatch and ExpressionSet. but I wanted to find some pictures about the classes hierarchy for more readable and understandable one. and, why I converted the probe-level data into the probeset data was that I wanted to compare those data by looking directly in excel file. but I can't find how to write the excel file from probe-leve data of the AffyBatch Object. so I tried to do it. and I wanted that it was possible to copy or convert from affybatch object to expression data with some modification directly but without normalization. sincerely Minwook On 8/22/07, Jenny Drnevich <drnevich at="" uiuc.edu=""> wrote: > Hi Min Wook, > > The discrepancy is because you are comparing the probe-level data > from an AffyBatch object to the probeset-level data of an > ExpressionSet created by gcrma(). Why would you want to convert an > AffyBatch object directly into an ExpressionSet object without > summarizing the probe-level data into probeset data? The AffyBatch > object extends the ExpressionSet structure specifically for > probe-level data (individual PM and MM intensities), and typically > ExpressionSet objects are reserved for summarized probeset data. For > more details on the data classes, use ?"AffyBatch" and ?"ExpressionSet". > > Cheers, > Jenny > > At 11:42 AM 8/22/2007, Min Wook Kim 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.UT F-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" > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > >

Excel 2007 has more than 1 million rows now. Weiyin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W. MacDonald Sent: Thursday, August 23, 2007 11:09 AM To: Jenny Drnevich Cc: lgautier at altern.org; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] how to convert a AffyBatch into ExpressionSet object ? Jenny Drnevich wrote: >>> and, why I converted the probe-level data into the probeset data was >>> that I wanted to compare those data by looking directly in excel file. >>> but I can't find how to write the excel file from probe-leve data of >>> the AffyBatch Object. so I tried to do it. >> What about the following ? >> write.csv(exprs(abatch), file="myProbeLevelData.csv") > > Be aware that you won't be able to use Excel to look at probe-level > data because Excel maxes out at ~65,000 rows (unless they've changed > something recently). My understanding is that Excel 2007 has increased the number of rows, but I couldn't find anything with a google search to back that up. > >>> and I wanted that it was possible to copy or convert from affybatch >>> object to expression data with some modification directly but without >>> normalization. >> Did you try this ? >> help("expresso", package="affy") >> > > There are also functions you can use to just do background correction > or normalization without summarization, if you want to see what > effect they have. See ?bg.adjust.gcrma for gc-based background > correction, ?bg.correct for other bg correction methods, and > ?normalize.methods for normalization options. expresso() is nice in > that it lets you mix-and-match between a variety of different bg > corrections, normalizations and summarization methods, and rma() and > gcrma() have arguments to turn off the background correction and/or > normalization. > > > Cheers, > Jenny > > >> Hoping this helps, >> >> >> >> Laurent >> >> >> >>> sincerely >>> Minwook >>> >>> On 8/22/07, Jenny Drnevich <drnevich at="" uiuc.edu=""> wrote: >>>> Hi Min Wook, >>>> >>>> The discrepancy is because you are comparing the probe-level data >>>> from an AffyBatch object to the probeset-level data of an >>>> ExpressionSet created by gcrma(). Why would you want to convert an >>>> AffyBatch object directly into an ExpressionSet object without >>>> summarizing the probe-level data into probeset data? The AffyBatch >>>> object extends the ExpressionSet structure specifically for >>>> probe-level data (individual PM and MM intensities), and typically >>>> ExpressionSet objects are reserved for summarized probeset data. For >>>> more details on the data classes, use ?"AffyBatch" and ?"ExpressionSet". >>>> >>>> Cheers, >>>> Jenny >>>> >>>> At 11:42 AM 8/22/2007, Min Wook Kim 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.U TF -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" >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> Jenny Drnevich, Ph.D. >>>> >>>> Functional Genomics Bioinformatics Specialist >>>> W.M. Keck Center for Comparative and Functional Genomics >>>> Roy J. Carver Biotechnology Center >>>> University of Illinois, Urbana-Champaign >>>> >>>> 330 ERML >>>> 1201 W. Gregory Dr. >>>> Urbana, IL 61801 >>>> USA >>>> >>>> ph: 217-244-7355 >>>> fax: 217-265-5066 >>>> e-mail: drnevich at uiuc.edu >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor