[BioC] boxplots on summarized data

[Jenny Drnevich]

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
>
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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.
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e-mail: drnevich at uiuc.edu