Comments (1)
Thank you for your interest in our work. A couple of suggestions that might help:
- Regarding the installation of the original version of powsim, I suggest you bring it up with the powsim developers. As far as I can see, there are a number of differences between powsim and powsimR, and I can not guarantee that our code will work as-is with powsimR.
- The MultiAssayExperiment objects were indeed created with R 3.3.2. However, you can download updated objects from conquer (http://imlspenticton.uzh.ch:3838/conquer/) for most of the data sets.
- The "assay column not a factor" error is related to a change in the validity checks in the MultiAssayExperiment package (waldronlab/MultiAssayExperiment#206). If you explicitly turn the column into a factor I think it should work (see e.g. https://github.com/csoneson/conquer_comparison/blob/master/scripts/prepare_mae.R)
- You can get DEsingle here: https://github.com/miaozhun/DEsingle
- NODES is provided as an archive by the authors (link from their bioRxiv preprint: https://www.dropbox.com/s/pno78mmlj0exv7s/NODES_0.0.0.9010.tar.gz?dl=0)
Hope this helps
Charlotte
from conquer_comparison.
Related Issues (9)
- A quick question on constructing "L" object HOT 3
- Creating Data obj, L HOT 3
- cell_cycle_geneids.rds HOT 1
- Add a new DE method HOT 2
- Difficulty in running the script HOT 8
- Prefiltering of lowly expressed genes HOT 11
- Simulation method used for the signal datasets? HOT 3
- Description of the results data HOT 1
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from conquer_comparison.