[BioC] Bug in vsn2

"M. Gonzalo Claros Díaz" claros at uma.es
Tue Jul 14 22:38:40 CEST 2009

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=  

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"))


 > sessionInfo()
R version 2.9.0 (2009-04-17)


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            
[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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