Difficulty in getting a boxplot display of nomralized data using affy
2
0
Entering edit mode
@richard-friedman-513
Last seen 10.2 years ago
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
Cancer cdf affy Cancer cdf affy • 1.5k views
ADD COMMENT
0
Entering edit mode
Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.2 years ago
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?
ADD COMMENT
0
Entering edit mode
@julia-engelmann-559
Last seen 10.2 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 390 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6