[BioC] boxplot expressionset

David martin vilanew at gmail.com
Wed Sep 1 11:49:33 CEST 2010


#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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