Hi Boris, For the hist, try plotHist() in the affycoretools package to automagically get a legend and colors, or you can do it the way Martin suggested which lets you have more control over what is plotted. I'm not sure why you would want to use the image on an ExpressionSet object, but the affyPLM package has a good way to plot the residuals left after fitting a pre-processing algorithm so you can more easily see spatial effects on your arrays; see the QC assessment vignette of affyPLM (athough it's missing in my current R installation - I'll post a separate thread about it). Finally, for the boxplot you can do: > boxplot(data.frame(exprs(e)) Cheers, Jenny At 11:48 PM 3/2/2009, Martin Morgan wrote: >Hi Boris -- > >Boris Umylny <umylny at="" apbri.org=""> writes: > > > Hi, > > > > I am working with affy library from Bioconductor 2.3. > > > > The library contains functions (hist, image and boxplot) that > work directly on > > AffyBatch object, but apparently not on ExpressionSet/eSet > object. After I > > use rma, expresso or mas5 to do background correction and > normalization I get > > an eSet object, which appears to be incompatible with these > functions. If I > > call hist(exprs(e)), where e is an ExpressionSet object, I get a > plot of the > > first array only. > > > > Is there a Bioconductor library (other than geneplotter which > apparently does > > not) that provides these functions on eSet/ExpressionSet object? > >Others will probably point to specific packages implementing plotting >methods for expression data, but I find myself doing things more >directly, typically using the lattice package > > library(lattice) > library(Biobase) > data(sample.ExpressionSet) > eset <- sample.ExpressionSet # easier to type! > df <- data.frame(Expression=as.vector(exprs(eset)), > Sample=sampleNames(eset)[col(eset)]) > densityplot(~log2(Expression)|Sample, df, plot.points=FALSE) > >or > > densityplot(~log2(Expression), group=Sample, df, plot.points=FALSE) > > > Is there a way to get an AffyBatch object from eSet object to make use of > > these functions? > >An AffyBatch and an ExpressionSet are conceptually different ('raw' >vs. preprocessed data) so trying to convert back and forth at will >doesn't really make sense. > >Martin > > > Thank you in advance for your help. > > > > > > Sincerely, > > > > > > Boris Umylny > > > > _______________________________________________ > > 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 > >-- >Martin Morgan >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M2 B169 >Phone: (206) 667-2793 > >_______________________________________________ >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 illinois.edu

Thank you very much for your help! I wound up using Martin's suggestion for density and boxplots. As Jenny pointed out it does not make much sense to run image on an ExpressionSet. However, that does require users to utilize AffyRead even if they are processing their data with just.rma. However, thats not a major obtacle. I did find a strange error with just.rma when reading gzipped CEL files from GSE10641 (samples GSM268225, GSM268224, GSM268223, GSM268222, GSM268221, GSM268214, GSM268213, GSM268212, GSM268211, GSM268210, GSM268209, GSM268226, GSM268233, GSM268234, GSM268235, GSM268236, GSM268237, GSM268238) with normalize=FALSE: Error in dimnames(x) <- dn : 'dimnames' applied to non-array and ExpressionSet was not created. When I used AffyRead and rma (with normalize=FALSE), it worked fine. I am using R 2.8.1, Bioconductor 2.3 and including: library(affy) library(geneplotter) library(lattice) library(Biobase) Thank you again for your help! Sincerely, Boris Umylny On Tuesday 03 March 2009 02:48:13 pm Martin Morgan wrote: > Hi Boris -- > > Boris Umylny <umylny at="" apbri.org=""> writes: > > Hi, > > > > I am working with affy library from Bioconductor 2.3. > > > > The library contains functions (hist, image and boxplot) that work > > directly on AffyBatch object, but apparently not on ExpressionSet/eSet > > object. After I use rma, expresso or mas5 to do background correction > > and normalization I get an eSet object, which appears to be incompatible > > with these functions. If I call hist(exprs(e)), where e is an > > ExpressionSet object, I get a plot of the first array only. > > > > Is there a Bioconductor library (other than geneplotter which apparently > > does not) that provides these functions on eSet/ExpressionSet object? > > Others will probably point to specific packages implementing plotting > methods for expression data, but I find myself doing things more > directly, typically using the lattice package > > library(lattice) > library(Biobase) > data(sample.ExpressionSet) > eset <- sample.ExpressionSet # easier to type! > df <- data.frame(Expression=as.vector(exprs(eset)), > Sample=sampleNames(eset)[col(eset)]) > densityplot(~log2(Expression)|Sample, df, plot.points=FALSE) > > or > > densityplot(~log2(Expression), group=Sample, df, plot.points=FALSE) > > > Is there a way to get an AffyBatch object from eSet object to make use of > > these functions? > > An AffyBatch and an ExpressionSet are conceptually different ('raw' > vs. preprocessed data) so trying to convert back and forth at will > doesn't really make sense. > > Martin > > > Thank you in advance for your help. > > > > > > Sincerely, > > > > > > Boris Umylny > > > > _______________________________________________ > > 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

Martin, Let me apologize in advance if I made a silly mistake - my programming skills are fairly limited. I've attached two files to this e-mail. R.in contains the R script and R.out is the screen capture of the output produced by the script. R command was invoked with "--vanilla". Both files are in Linux text forma. I am using SUSE Linix 10.3. Sincerely, Boris Umylny On Friday 06 March 2009 11:47:34 pm Martin Morgan wrote: > Hi Boris -- > > Boris Umylny <umylny at="" apbri.org=""> writes: > > Thank you very much for your help! > > > > I wound up using Martin's suggestion for density and boxplots. As Jenny > > pointed out it does not make much sense to run image on an ExpressionSet. > > However, that does require users to utilize AffyRead even if they are > > processing their data with just.rma. However, thats not a major obtacle. > > > > I did find a strange error with just.rma when reading gzipped CEL files > > from GSE10641 (samples GSM268225, GSM268224, GSM268223, GSM268222, > > GSM268221, GSM268214, GSM268213, GSM268212, GSM268211, GSM268210, > > GSM268209, GSM268226, GSM268233, GSM268234, GSM268235, GSM268236, > > GSM268237, GSM268238) with normalize=FALSE: > > > > Error in dimnames(x) <- dn : 'dimnames' applied to non-array > > > > and ExpressionSet was not created. > > > > When I used AffyRead and rma (with normalize=FALSE), it worked fine. > > Unfortunately, I don't see this problem when I try with R 2.8.0 or > R-devel. To track it down further it would really help to see the > output of sessionInfo() (after following the instructions to update > packages at http://bioconductor.org/docs/install/ and confirming that > the error still occurs) and the precise command that you used. Here's > mine... > > > setwd("~/tmp/GEO") > > f <- c("GSM268225", "GSM268224", "GSM268223", "GSM268222", "GSM268221", > > "GSM268214", "GSM268213", "GSM268212", "GSM268211", "GSM268210", > > "GSM268209", "GSM268226", "GSM268233", "GSM268234", "GSM268235", > > "GSM268236", "GSM268237", "GSM268238") f <- paste(f, ".CEL.gz", sep="") > > all(f %in% list.files()) > > [1] TRUE > > > res <- justRMA(filenames=f, normalize=FALSE) > > sessionInfo() > > R version 2.8.0 Patched (2008-11-10 r46882) > x86_64-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME= C;LC_AD >DRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics utils datasets > grDevices methods > [8] base > > other attached packages: > [1] rat2302cdf_2.3.0 affy_1.20.2 Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 preprocessCore_1.4.0 > > Martin > > > I am using R 2.8.1, Bioconductor 2.3 and including: > > > > library(affy) > > library(geneplotter) > > library(lattice) > > library(Biobase) > > > > > > Thank you again for your help! > > > > > > Sincerely, > > > > > > Boris Umylny > > > > On Tuesday 03 March 2009 02:48:13 pm Martin Morgan wrote: > >> Hi Boris -- > >> > >> Boris Umylny <umylny at="" apbri.org=""> writes: > >> > Hi, > >> > > >> > I am working with affy library from Bioconductor 2.3. > >> > > >> > The library contains functions (hist, image and boxplot) that work > >> > directly on AffyBatch object, but apparently not on ExpressionSet/eSet > >> > object. After I use rma, expresso or mas5 to do background correction > >> > and normalization I get an eSet object, which appears to be > >> > incompatible with these functions. If I call hist(exprs(e)), where e > >> > is an ExpressionSet object, I get a plot of the first array only. > >> > > >> > Is there a Bioconductor library (other than geneplotter which > >> > apparently does not) that provides these functions on > >> > eSet/ExpressionSet object? > >> > >> Others will probably point to specific packages implementing plotting > >> methods for expression data, but I find myself doing things more > >> directly, typically using the lattice package > >> > >> library(lattice) > >> library(Biobase) > >> data(sample.ExpressionSet) > >> eset <- sample.ExpressionSet # easier to type! > >> df <- data.frame(Expression=as.vector(exprs(eset)), > >> Sample=sampleNames(eset)[col(eset)]) > >> densityplot(~log2(Expression)|Sample, df, plot.points=FALSE) > >> > >> or > >> > >> densityplot(~log2(Expression), group=Sample, df, plot.points=FALSE) > >> > >> > Is there a way to get an AffyBatch object from eSet object to make use > >> > of these functions? > >> > >> An AffyBatch and an ExpressionSet are conceptually different ('raw' > >> vs. preprocessed data) so trying to convert back and forth at will > >> doesn't really make sense. > >> > >> Martin > >> > >> > Thank you in advance for your help. > >> > > >> > > >> > Sincerely, > >> > > >> > > >> > Boris Umylny > >> > > >> > _______________________________________________ > >> > 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 -------------- next part -------------- library(affy) library(geneplotter) library(lattice) library(Biobase) e <- just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz","/home/umyln y/tmp/rat_cel/GSM268210.CEL.gz","/home/umylny/tmp/rat_cel/GSM268211.CE L.gz","/home/umylny/tmp/rat_cel/GSM268212.CEL.gz","/home/umylny/tmp/ra t_cel/GSM268213.CEL.gz","/home/umylny/tmp/rat_cel/GSM268214.CEL.gz","/ home/umylny/tmp/rat_cel/GSM268221.CEL.gz","/home/umylny/tmp/rat_cel/GS M268222.CEL.gz","/home/umylny/tmp/rat_cel/GSM268223.CEL.gz","/home/umy lny/tmp/rat_cel/GSM268224.CEL.gz","/home/umylny/tmp/rat_cel/GSM268225. CEL.gz","/home/umylny/tmp/rat_cel/GSM268226.CEL.gz","/home/umylny/tmp/ rat_cel/GSM268233.CEL.gz","/home/umylny/tmp/rat_cel/GSM268234.CEL.gz", "/home/umylny/tmp/rat_cel/GSM268235.CEL.gz","/home/umylny/tmp/rat_cel/ GSM268236.CEL.gz","/home/umylny/tmp/rat_cel/GSM268237.CEL.gz","/home/u mylny/tmp/rat_cel/GSM268238.CEL.gz", normalize=FALSE) sessionInfo() -------------- next part -------------- WARNING: ignoring environment value of R_HOME R version 2.8.1 (2008-12-22) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(geneplotter) Loading required package: lattice Loading required package: annotate Loading required package: AnnotationDbi Loading required package: xtable KernSmooth 2.22 installed Copyright M. P. Wand 1997 > library(lattice) > library(Biobase) > e <- just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz","/home/umy lny/tmp/rat_cel/GSM268210.CEL.gz","/home/umylny/tmp/rat_cel/GSM268211. CEL.gz","/home/umylny/tmp/rat_cel/GSM268212.CEL.gz","/home/umylny/tmp/ rat_cel/GSM268213.CEL.gz","/home/umylny/tmp/rat_cel/GSM268214.CEL.gz", "/home/umylny/tmp/rat_cel/GSM268221.CEL.gz","/home/umylny/tmp/rat_cel/ GSM268222.CEL.gz","/home/umylny/tmp/rat_cel/GSM268223.CEL.gz","/home/u mylny/tmp/rat_cel/GSM268224.CEL.gz","/home/umylny/tmp/rat_cel/GSM26822 5.CEL.gz","/home/umylny/tmp/rat_cel/GSM268226.CEL.gz","/home/umylny/tm p/rat_cel/GSM268233.CEL.gz","/home/umylny/tmp/rat_cel/GSM268234.CEL.gz ","/home/umylny/tmp/rat_cel/GSM268235.CEL.gz","/home/umylny/tmp/rat_ce l/GSM268236.CEL.gz","/home/umylny/tmp/rat_cel/GSM268237.CEL.gz","/home /umylny/tmp/rat_cel/GSM268238.CEL.gz", normalize=FALSE) Error in dimnames(x) <- dn : 'dimnames' applied to non-array In addition: Warning message: In just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz", "/home/umylny/tmp/rat_cel/GSM268210.CEL.gz", : Incompatible phenoData object. Created a new one. > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rat2302cdf_2.3.0 geneplotter_1.20.0 annotate_1.20.1 [4] xtable_1.5-4 AnnotationDbi_1.4.3 lattice_0.17-17 [7] affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 DBI_0.2-4 grid_2.8.1 [4] KernSmooth_2.22-22 preprocessCore_1.4.0 RColorBrewer_1.0-2 [7] RSQLite_0.7-1 >