[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

2015-12-17 Thread Ludwig Geistlinger
Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

2015-12-17 Thread Obenchain, Valerie
Thanks! Valerie On 12/17/2015 08:32 AM, Brad Friedman wrote: > Thanks, I've made the corresponding change to release version, and > bumped minor version there. > > I previously only made it to devel. > > Brad > > On Thu, Dec 17, 2015 at 8:21 AM, Obenchain, Valerie >

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

2015-12-17 Thread Obenchain, Valerie
Hi Brad, Following up on this because AnalysisPageServer is still broken in release. Can you please fix? Thanks. Valerie On 12/14/2015 01:36 PM, Morgan, Martin wrote: > At least for the R package side of things, I think the question of how to > invoke R CMD in a Makefile is moot for

Re: [Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

2015-12-17 Thread Brad Friedman
Thank YOU!!! Bioconductor is fantastic. Brad Friedman 617-230-7055 > On Dec 17, 2015, at 8:47 AM, "Obenchain, Valerie" > wrote: > > Thanks! > > Valerie > >> On 12/17/2015 08:32 AM, Brad Friedman wrote: >> Thanks, I've made the corresponding change to

Re: [Bioc-devel] seqlevelsStyle on alternate chromosomes

2015-12-17 Thread Leonardo Collado Torres
I've also found https://github.com/dpryan79/ChromosomeMappings useful On Thu, Dec 17, 2015 at 6:40 PM, Hervé Pagès wrote: > Hi Michael, > > On 12/17/2015 02:45 PM, Michael Lawrence wrote: >> >> Seems like seqlevelsStyle<- between e.g. UCSC and NCBI does not work >> outside

Re: [Bioc-devel] seqlevelsStyle on alternate chromosomes

2015-12-17 Thread Hervé Pagès
Hi Michael, On 12/17/2015 02:45 PM, Michael Lawrence wrote: Seems like seqlevelsStyle<- between e.g. UCSC and NCBI does not work outside of the "standard" chromosomes. Since GRCh38 (NCBI) and hg38 (UCSC) are the same assembly, we could probably implement a complete mapping, right?