Yes, a "readSummarizedExperiment" would be a "modern-day analog of Biobase::readExpressionSet". I also agree with the other suggestions including github to get this started, and Vince's thoughts on binding meta-data more tightly to source data as well as improving interoperability.
As suggested I am sharing this discussion with the bioc-devel list. Thomas On Wed, Jun 29, 2016 at 06:22:49PM +0000, Vincent Carey wrote: > Thanks Thomas -- I think this should be circulated to biocore for further > comments. I am in agreement > that we need to do a better job at both demonstrating the values of a) > binding metadata to data, b) > using standard containers through workflows, c) allowing interoperation. I > learned some useful things > about spreadsheet interoperation at the conference and need to learn more. > > In a sense we are giving a specific implementation of some of the rules in > > http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285 > > and I wonder whether we could come up with another topic for the "ten simple > rules" > series that addresses these concerns, or do something similar, perhaps for > F1000Research, > with a Bioconductor-interoperability focus on metadata. > On Wed, Jun 29, 2016 at 06:28:49PM +0000, Martin Morgan wrote: > I guess you mean a modern-day analog of Biobase::readExpressionSet ? I > like the idea of templates, and also drafting a 'Ten Steps Toward > Reproduciblity in R / Bioconductor'. Would be happy to start a github > repo for same if there are any takers... > > Martin > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee > or agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > On 06/29/2016 01:57 PM, Thomas Girke wrote: > > Hi Vince and Martin, > > > > It was great seeing you at the Bioc conference, and thanks for all your > > time organizing the conference. As always it was a great success with a > > lot of inspiring presentations and discussions. > > > > In one of our discussions you ask me for feedback why I think handling > > of meta-data is currently not straightforward for non-expert users of > > Bioc packages such as biologists, data analysts or developers coming > > from other languages. > > > > In my opinion, one main reason for this difficulty is that there is no > > formal utility provided for importing meta-data from external files > > (e.g. tabular, json or other formats). SummarizedExperiments has all > > these great functionalities but it is not intuitive to non-expert users > > how to import the data into the final object. For a developer it is easy > > to write a custom import function but not to non-R programmers. > > Addressing this need would be trivial by providing an import function > > that could read meta-data (optionally along with assay/range data) > > provided by the user directly into SummarizedExperiment objects (and/or > > RangedSummarizedExperiment). To the best of my knowledge, a > > readSummarizedExperiment is currently not available, but I might be wrong? > > > > Almost equally important would be an export function so that users can > > easily report intermediate results and also share them with external > > software outside of R. Clearly, for the latter need exporting to an Rd > > file is not an option. > > > > Especially the import step overlaps substantially how we communicate > > with experimentalists via spreadsheets, a topic we discussed at the > > meeting quite a bit. Providing one or two best practice templates of how > > to organize experiments in the 'spirit' of SummarizedExperiment could > > help to educate scientists how to format their meta-data in Excel or > > Google sheets so that they are easier to process. This would also > > improve reproducibility since many sample handling errors happen right > > at this level. As an example file one could use here the current colData > > sample used by the SummarizedExperiment vignette. > > > > That's really all. > > > > Best, > > > > Thomas > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel