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waldronlab / GSEABenchmarkeR

Reproducible GSEA Benchmarking
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Missing dataset ID in output files when runEA on a single SE #12

Closed lgeistlinger closed 4 years ago

lgeistlinger commented 4 years ago

When running runEA on just one SummarizedExperiment, the results are saved without the dataId of the dataset (i.e. just as .rds and .txt)

lgeistlinger commented 4 years ago

For this to work you need to either explicitly set:

metadata(se)$dataId <- "myDatasetId"
runEA(se, ...)

(or, alternatively, wrap the SE in a list via 

exp.list <- list(myDatasetId = se)
runEA(exp.list, ...)

)

lgeistlinger commented 4 years ago

My previous comment applies for the case of a single SE and a single method. I just observed when using multiple methods on a single SE (which I treat internally slightly different), the dataset ID is indeed missing.

I introduced a fix for that in GSEABenchmarkeR v1.7.3, which you can download directly from github via:

BiocManager::install("waldronlab/GSEABenchmarkeR")

(requires that you have the remotes package installed)