Bug in vsn2
1
0
Entering edit mode
@-m-gonzalo-claros-diaz-2184
Last seen 8.4 years ago
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/
limma marray limma marray • 1.1k views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 2 days ago
EMBL European Molecular Biology Laborat…
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
ADD COMMENT

Login before adding your answer.

Traffic: 389 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6