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waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data
https://waldronlab.io/MultiAssayExperiment/
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nested experiments #258

Closed phaverty closed 5 years ago

phaverty commented 5 years ago

Good morning. I've been working a lot with MAE recently. Thanks for making it! It looks like MAE doesn't like experiments to have more than one assay. I work a lot with Experiments that are SummarizedExperiments with multiple assay matrices. MAE features like assays and wideFormat seem to ignore all but the first matrix. Is this by design? (Am I doing it wrong?)

LiNk-NY commented 5 years ago

Hi Peter, @phaverty

I'm glad to hear you're making use of our software!

Yes, this is by design. Although there is an i argument in wideFormat, it gets passed to all assays so you would only use it if all SummarizedExperiments in the MultiAssayExperiment have the (at least) same number of assays as i BUT it will only extract that particular assay. I would recommend to separate these out into separate assays in the ExperimentList. You could also use the c method for MultiAssayExperiment to append those additional experiments based on an existing experiment.

Best regards, Marcel

stale[bot] commented 5 years ago

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