Levi Waldron
Levi Waldron
Also, I noticed that my little hack of getting rid of the `--user` flag doesn't help for my rstudio-server command from the waldronlab/bioconductor crate, which doesn't contain the user flag...
I'm using the create directly from https://github.com/databio/hub.bulker.io/blob/master/waldronlab/bioconductor.yaml, so I guess that's why the user mapping isn't present in my rstudio-server bulker script? Here's the full diff on those scripts: ```...
This is not high priority but I still think it would be a good learning exercise. @cmirzayi it might actually be even more immediately relevant to you if you feel...
Oh great, sorry I missed those!
Likely cause - the `relab_sub_t_df`in the call `raw_lda_scores
Actually these relative abundances are correct, I forgot that they are scaled to add to 1e6. I think this is real collinearity, caused by the presence of synthetic clades (e.g....
(used to be, "consider using `scater::runPCA` / `scater::calculatePCA`", changed after discussion with Vince). `irlba` has an advantage of only one dependency (`Matrix`), and allowing computation of only the desired number...
@HelloWorldLTY you mentioned you were using a GPU, is that correct or is it a typo for CPU?
Also, could you try running the following benchmark? It would help to be sure that your time is actually being spent evaluating the heatmapTable function, and not something else cluster...
I assume it's because there have been more samples added to cMD since 2021, wouldn't worry about small changes in the coefficients.