[BioC] Bug in vsn2

[Wolfgang Huber]

Dear Gonzalo,

thank you for reporting this. vsn2 actually uses the coercion method 
from RGList to NchannelSet from the convert package when presented with 
an RGList object, and I suspect the problem lies there.

In order to really diagnose (and fix) this problem, we would need a 
reproducible example. Can you make available, either to this list or me 
privately, your two objects RG and RG2 (or a method of re-creating 
them), as well as the code you use to call vsn2 and the error message 
you experience?

Currently, vsn2 will work with RGlist objects with slots R and G (and 
optionally Rb, Gb); and not otherwise.

	Thanks and best wishes
	Wolfgang


M. Gonzalo Claros Díaz wrote:
> I have found a bug in vsn2 function using RGList as input object.
> 
> I have constructed a RGList object that includes an "other" slot with 
> read.maimages() from limma. When I use this object with vsn2 function, I 
> get a very strange hanging error.
> 
> When I run the same data *without* the "other" slot (by reading them 
> with different read.maimages parameters), it works fine.
> 
> This RGList works fine with vsn2:
> 
>     tg <- readTargets(targetF, row.names="SlideNumber")
>     RG <- read.maimages(tg$FileName, source="genepix.median", wt.fun= 
> FilterChip)
> 
> This RGList hangs vsn2 (but not the rest of calculations with limma and 
> marray package funtions):
> 
>     RG2 <- read.maimages(tg$FileName, source="genepix.median", wt.fun= 
> FilterChip, other.columns=c(snr532="SNR 532", snr635="SNR 635"))
> 
> Gonzalo
> 
>  > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
> 
> locale:
> es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] vsn_3.12.0    Biobase_2.4.1 marray_1.22.0 limma_2.18.0
> 
> loaded via a namespace (and not attached):
> [1] affy_1.22.0          affyio_1.12.0        grid_2.9.0           
> lattice_0.17-22
> [5] preprocessCore_1.6.0
> 
> -- 
> «Donde me he equivocado, soy el único responsable; donde no,
> el mérito es de los que me han ayudado»
> ================================================================
> M. Gonzalo CLAROS                                  claros at uma.es
> Dpt. Biología Molecular y Bioquímica
> Facultad de Ciencias                      Fax: (+34) 95 213 2041
> Universidad de Málaga                Tel: (+34) 95 213 7284/7653
> E-29071 Málaga (Spain)               http://www.bmbq.uma.es/fmp/
> 
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-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber