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 ?nico responsable; donde no, el m?rito es de los que me han ayudado? ================================================================ M. Gonzalo CLAROS claros at uma.es Dpt. Biolog?a Molecular y Bioqu?mica Facultad de Ciencias Fax: (+34) 95 213 2041 Universidad de M?laga Tel: (+34) 95 213 7284/7653 E-29071 M?laga (Spain) http://www.bmbq.uma.es/fmp/

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 D?az 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 ?nico responsable; donde no, > el m?rito es de los que me han ayudado? > ================================================================ > M. Gonzalo CLAROS claros at uma.es > Dpt. Biolog?a Molecular y Bioqu?mica > Facultad de Ciencias Fax: (+34) 95 213 2041 > Universidad de M?laga Tel: (+34) 95 213 7284/7653 > E-29071 M?laga (Spain) http://www.bmbq.uma.es/fmp/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber