[BioC] boxplot expressionset
axel.klenk at actelion.com
axel.klenk at actelion.com
Wed Sep 1 13:00:58 CEST 2010
Hi David,
normally, read.table() makes a good guess at the
data types of your file's columns, so something
in your data file must be causing it to go wrong.
Look at your data file and the arguments in ?read.table
especially na.strings, colClasses, and comment.char
can be useful.
If you cannot identify the problem, show us the data file,
96x12 is not too large...
Cheers,
- axel
Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland
From:
David martin <vilanew at gmail.com>
To:
bioconductor at stat.math.ethz.ch
Date:
01.09.2010 11:51
Subject:
Re: [BioC] boxplot expressionset
Sent by:
bioconductor-bounces at stat.math.ethz.ch
#Data is imported this way
mydataFile=read.table(file=data,header=TRUE,row.names=2,sep="\t",
as.is=TRUE,check.names=FALSE)
> is.character(exprs(mydata.eset))
[1] TRUE
>exprs(mydata.eset)[1,1]
[1] "35.7403" #should be 35.7 (no quotes)
I guess i need to transform data into numeric during import ?? am i
right ? IS it possible to do that from the expressionset object ?
thanks,
On 01/09/10 11:37, axel.klenk at actelion.com wrote:
> Hi David,
>
> where does your ExpressionSet come from? -- It contains
> character data and that is the cause of the error in boxplot().
>
> Cheers,
>
> - axel
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
>
>
>
>
> From:
> David martin<vilanew at gmail.com>
> To:
> bioconductor at stat.math.ethz.ch
> Date:
> 01.09.2010 11:28
> Subject:
> [BioC] boxplot expressionset
> Sent by:
> bioconductor-bounces at stat.math.ethz.ch
>
>
>
> Hi,
> I have an expressionset object:
>
> str(exprs(mydata.eset))
> chr [1:96, 1:12] "35.7403" "32.772404" "31.26038" "45" ...
> - attr(*, "dimnames")=List of 2
> ..$ : chr [1:96] "geneA" "geneB" "geneC" "geneD" ...
> ..$ : chr [1:12] "SampleA" "SampleB" "SampleC" "SampleD" ...
>
> The object contais 96 genes and 12 samples. How to boxplot the object
> > boxplot(exprs(mydata.eset))
> Error in x[floor(d)] + x[ceiling(d)] :
> non-numeric argument to binary operator
>
> thanks for your help.
>
> david
>
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