Good day, You are operating with tables of statistical hypothesis test summaries, rather than input data which the tests are done with, so it doesn't make sense to use SummarizedExperiment or MultiAssayExperiment. The data is not experimental measurements. You should try DataFrame from Bioconductor package S4Vectors. It's better than a data.frame and won't flood your console with output. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia
[Bioc-devel] Use of SummerisedExperiments or MultiAssayExperiments of many many Dataframes/ nested List objects
2 messages · Dario Strbenac, Levi Waldron
2 days later
Krutik, what's the link to your package submission issue on GitHub? I feel I would need a little more information on the package to give my opinion or advice. It is true that SummarizedExperiment and MultiAssayExperiment are designed primarily for experimental data rather than for differential expression output. But my first impression is that it will be important for you to directly support output from DESeq2, edgeR, and limma, since those are where most Bioconductor users get differential expression output from.
Levi Waldron Associate Professor Department of Epidemiology and Biostatistics CUNY Graduate School of Public Health and Health Policy Institute for Implementation Science in Population Health 55 W 125th St, New York NY 10035 https://waldronlab.io [[alternative HTML version deleted]]