[BioC] boxplot expressionset

[axel.klenk at actelion.com]

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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The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by letter.
Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com