That's it, thanks for the quick reply. Dennis Burian, Ph.D. Functional Genomics Group Civil Aerospace Medical Institute, AAM-610 6500 S. MacArthur Blvd. Oklahoma City OK 73169 405-954-6087 dennis.burian at faa.gov Jenny Drnevich <drnevich at="" uiuc.ed="" u=""> To Dennis M Burian/AMC/FAA at FAA, 01/22/2008 03:15 Bioconductor at stat.math.ethz.ch PM cc Subject Re: [BioC] boxplots on summarized data Hi Dennis, In all your examples you aren't subsetting the exprs matrix correctly - it has two dimensions, but you're only subsetting on one. First of all, > exprs(x)[10:20] doesn't give you the data for those 11 genes in a table, it only returns the data for those genes from the first array. However, that may not be your only problem. Let me make sure I understand what you want to do: for each gene you want one box showing the mean, percentiles, etc. for the group of arrays, and all these boxes on one plot. Working through an example: >exprs(x)[10:20 , 1:5] This gives you the data matrix of genes 10-20 on arrays 1-5, but doing this: >boxplot(exprs(x)[10:20 , 1:5]) combines all the values into one boxplot because exprs(x) is a matrix. Next step: >boxplot(data.frame(exprs(x)[10:20 , 1:5])) Now you have multiple boxes, but they are for each array, not each gene, so you have to transpose the data: >boxplot(data.frame(t(exprs(x)[10:20 , 1:5]))) Is what you want? Cheers, Jenny boxplot(data.frame(exprs(x)[10:20,] At 02:44 PM 1/22/2008, Dennis.Burian at faa.gov wrote: >I'm having a time generating boxplots across chips on summarized data for >more than one gene at a time. I want a set of boxplots for a subset of the >genes, say the 10th to the 20th genes in the ExpressionSet. I expect this >is an R list question but since the data is an expression set decided to >post it here instead. > >I've tried: >boxplot(exprs(x)[10:20]) >boxplot(exprs(x)[10,:20,]) >boxplot(exprs(x)c(10,11,12,13,14,15,16,17,18,19,20)) >these all return a single boxplot with the expression values for all chips >from all 11 genes in the same boxplot. > >boxplot(exprs(x)[10]) gives me a boxplot for one gene. >exprs(x)[10:20] returns the data for the 11 genes in a table. > >R 2.6.0 >x86_64-unknown-linux-gnu >Biobase_1.16.1 affy_1.16.0 > >I thought I had some understanding of subsetting and the last line of code >to get just the tabular data back validated that thought but now I'm mostly >just confused. > >thanks, DB > >Dennis Burian, Ph.D. >Functional Genomics Group >Civil Aerospace Medical Institute, AAM-610 >6500 S. MacArthur Blvd. >Oklahoma City OK 73169 >405-954-6087 >dennis.burian at faa.gov > >_______________________________________________ >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