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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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SingleCellExperiment (scater) #9

Closed katieburnham closed 6 years ago

katieburnham commented 6 years ago

I tried running the example code from the vignette, and get the following error with the estimateParam function:

Error in .run.checkup(countData = countData, batchData = batchData, spikeData = spikeData, : no slot of name "assayData" for this object of class "SingleCellExperiment" In addition: Warning message: 'newSCESet' is deprecated. Use 'SingleCellExperiment' instead. See help("Deprecated")

It looks like this may be due to an update in the scater package? (Running R 3.4.2 on Windows)

bvieth commented 6 years ago

Dear Katie,

thank you for trying powsimR. With the new Bioconductor release, some functions previously defined in scater moved to an auxillary package (SingleCellExperiment). I have changed my functions now accordingly.

Thanks for pointing this out and my apologies for the late answer, I was travelling.

I will close the issue, but feel free to reopen if needed!

Kind regards Beate