[BioC] oligo boxplot bug?

[Benilton Carvalho]

Hi Farhad,

I'll upload a fix very soon.

Thank you for the report.

b

On Aug 19, 2009, at 1:24 PM, Farhad Imam wrote:

> Dear list,
>
> I am using an ExpressionSet and generating figures using subsets of  
> genes via boxplot (oligo) and plotlines (limma).
>
>> class(zf.rma.sub1)
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>
> My data in the expression set is log2-transformed, as expected:
>
>> exprs(zf.rma)[1:3,1:2]
>         220302_4-24-08_1cell_0004_532.xys  
> 220302_4-24-08_1cell_0004_635.xys
> AA494792                         14.730366                          
> 14.623973
> AA494800                         14.314152                          
> 13.728564
> AA494831                          6.960698                           
> 6.748818
>
> My lineplots also look fine, but for some reason the y-axis on my  
> boxplots automatically converts to log10 and I can only fix it by  
> doing something stupid and clunky like this after I call the boxplot:
>
> axis(2, at=c(3.0,3.2,3.4,3.6,3.8,4.0),   
> lab=c("6","8","10","12","14","16"))
>
> which isn't actually precise anway. Any ideas?
>
> Many thanks,
>
> Farhad Imam
>
> --------------------------------------------------
> Farhad Imam, MD, PhD
> Postdoctoral Fellow, Schier Lab
> Department of Molecular and Cellular Biology
> Harvard University
>
> (617) 496-4910
> fimam at mcb.harvard.edu
>
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