Dear Bioconductor users, I am currently running the latest version of affy 1.4.22 under R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the unnormalized data but not on the normalized data. Here are excerpts from my session: > howard1.raw AffyBatch object size of arrays=640x640 features (67206 kb) cdf=MG_U74Av2 (12488 affyids) number of samples=21 number of genes=12488 annotation=mgu74av2 > howard1.norm <- rma(howard1.raw) > howard1.norm Expression Set (exprSet) with 12488 genes 21 samples phenoData object with 1 variables and 21 cases varLabels sample: arbitrary numbering > boxplot(howard1.raw) Yielded a boxplot. But > boxplot(howard1.norm) Error in boxplot.default(howard1.norm) : invalid first argument Question: Should the rma normalized file be displayed by boxplot with the commands that I have typed? If not: Is there a way to display a boxplot of the normalized file? If so: any suggestions. In addition to affy, I so far have the following packages installed in my Library: [bb01friedman1:~/Library/R/library] friedman% ls Biobase R.css affy affyPLM affycomp liblisting.Rda mgu74av2cdf reposTools Do I need anything else to run box plot on the normalized object? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "'Chutes and Ladders' teaches cause and effect." - Rose Friedman, age 7 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2149 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040429/929699f4/attachment.bin

If you load the latest affyPLM, then you should be able to boxplot an exprSet in the same manner as a AffyBatch. > If not: Is there a way to display a boxplot of the normalized file?

Hi Richard, for me it works with: > boxplot(data.frame(exprs(howard1.norm)), names=c("Exp1","Exp2","Exp3","Exp4")) Note that if you want to use the "names" argument you must specify a name for each array (4 in my example ). Hope that helps, Julia On Thursday 29 April 2004 21:47, Richard Friedman wrote: > Dear Bioconductor users, > > I am currently running the latest version of affy 1.4.22 under > R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the unnormalized > data > > but not on the normalized data. Here are excerpts from my session: > > howard1.raw > > AffyBatch object > size of arrays=640x640 features (67206 kb) > cdf=MG_U74Av2 (12488 affyids) > number of samples=21 > number of genes=12488 > annotation=mgu74av2 > > > howard1.norm <- rma(howard1.raw) > > howard1.norm > > Expression Set (exprSet) with > 12488 genes > 21 samples > phenoData object with 1 variables and 21 cases > varLabels > sample: arbitrary numbering > > > boxplot(howard1.raw) > > Yielded a boxplot. > But > > > boxplot(howard1.norm) > > Error in boxplot.default(howard1.norm) : invalid first argument > > Question: Should the rma normalized file be displayed by boxplot with > the > commands that I have typed? > If not: Is there a way to display a boxplot of the normalized file? > If so: any suggestions. > In addition to affy, I so far have the following packages installed in > my Library: > [bb01friedman1:~/Library/R/library] friedman% ls > Biobase R.css affy affyPLM > affycomp liblisting.Rda mgu74av2cdf reposTools > > Do I need anything else to run box plot on the normalized object? > > Thanks and best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "'Chutes and Ladders' teaches cause and effect." - Rose Friedman, age 7