[Rd] arithmetic with zero-column data.frames

Should arithmetic operations work on zero-column data.frames (returning a zero-column data.frame with the same number of rows as the data.frame argument(s))? Currently we get: > 1 + data.frame(row.names=c("A","B")) Error in data.frame(value, row.names = rn, check.names = FALSE, check.rows =

Re: [Bioc-devel] Common Bioconductor Methods and Classes

For methods, I suggests writing that authors should look through BiocGenerics for things they ought to _think_ about. And emphasize that some of these methods probably does not make sense for many classes. Best, Kasper On Tue, Aug 8, 2017 at 10:28 AM, Michael Lawrence

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

Hi Gosia, I tried to reproduce your error. But I’m not sure there have been any changes on either your Github repo, or your SVN. Both repositories are at the exact same location right now. Please try these commands on a “fresh” clone of your GitHub repo. $ git clone

Re: [Bioc-devel] Common Bioconductor Methods and Classes

Looks like a good start. Would be nice to have some extra information (text description, some diagrams), and links to relevant documentation. On Tue, Aug 8, 2017 at 6:13 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Hello all, > > > Many have requested a page that helps identify

[Bioc-devel] Common Bioconductor Methods and Classes

Hello all, Many have requested a page that helps identify common Bioconductor methods and classes that should try to be utilized in package development. We have created the following webpage in the developers resources section of the website and links are also include in the

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

Hi Aaron and Martin, In any case, a distance matrix calculated from such an array would be fine, as long as the dimensions are equal to the number of cells. The question is whether it is needed by enough packages to warrant a slot in the base SCE class; I will discuss this with Davide and

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

On 08/08/2017 03:59 AM, Angerer, Philipp wrote: Hi Aaron, I guess this would be a question for the SummarizedExperiment developers, though personally, I never liked ExpressionSet's inclination to slap names on everything. Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”.

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

> I guess this would be a question for the > SummarizedExperiment developers, though personally, I never liked > ExpressionSet's inclination to slap names on everything. > > Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”. Since > they always refer to features and

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

On 08/08/2017 03:59 AM, Angerer, Philipp wrote: Hi Aaron, I guess this would be a question for the SummarizedExperiment developers, though personally, I never liked ExpressionSet's inclination to slap names on everything. Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”.

Re: [Bioc-devel] transitioning scater/scran to SingleCellExperiment

Hi Aaron, I guess this would be a question for the SummarizedExperiment developers, though personally, I never liked ExpressionSet's inclination to slap names on everything. Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”. Since they always refer to features and