[BioC] simpleaffy plot error

[Crispin Miller]

Hi Georg,
This is now fixed in the most recent updates to the devl and release
versions. It will appear soon on the downloads page.

release:  2.10.31
devl:     2.11.21


Crispin


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Georg Otto
> Sent: 22 May 2007 18:36
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] simpleaffy plot error
> 
> Dear Bioconductors,
> 
> since upgrading to R 2.5 and bioconductor 2.0, the 
> plot.qc.stats function of simpleaffy returns an error. I 
> attached the transcript of my session below. Could anybody 
> give me a hint what is going on?
> 
> Cheers,
> 
> Georg
> 
> 
> > Data
> AffyBatch object
> size of arrays=712x712 features (18 kb)
> cdf=Zebrafish (15617 affyids)
> number of samples=32
> number of genes=506944
> annotation=zebrafish
> notes=  
> 
> > qc<-qc(Data)
> > plot(qc)
> Error in rbind(c(), (vals[, p3] - vals[, p5])) : 
> 	invalid subscript
> 
> 
> > traceback()
> 7: rbind(c(), (vals[, p3] - vals[, p5]))
> 6: .getRatios(object)
> 5: ratios(x)
> 4: ratios(x)
> 3: plot.qc.stats(x, ...)
> 2: plot(qc)
> 1: plot(qc)
> 
> > sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-redhat-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
> TE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8
> ;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC
> _MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  
> "grDevices" "datasets" 
> [7] "utils"     "methods"   "base"     
> 
> other attached packages:
> zebrafishcdf   simpleaffy   genefilter     survival         
> affy       affyio 
>     "1.16.0"     "2.10.3"     "1.14.1"       "2.31"     
> "1.14.0"      "1.4.0" 
>      Biobase 
>     "1.14.0"
> 
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