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
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
>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?
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
>more than one gene at a time. I want a set of boxplots for a subset
>genes, say the 10th to the 20th genes in the ExpressionSet. I expect
>is an R list question but since the data is an expression set decided
>post it here instead.
>these all return a single boxplot with the expression values for all
>from all 11 genes in the same boxplot.
>boxplot(exprs(x)) gives me a boxplot for one gene.
>exprs(x)[10:20] returns the data for the 11 genes in a table.
>I thought I had some understanding of subsetting and the last line of
>to get just the tabular data back validated that thought but now I'm
>Dennis Burian, Ph.D.
>Functional Genomics Group
>Civil Aerospace Medical Institute, AAM-610
>6500 S. MacArthur Blvd.
>Oklahoma City OK 73169
>dennis.burian at faa.gov
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives:
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
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at uiuc.edu