Closed katimbach closed 10 months ago
Hi @katimbach ,
thanks for the detailed report.
Actually, you may have been affected by changes in the API and there are several arguments that start with reduction (reduction.use and reduction.save). To fix this, you need to be explicit about which one you are choosing. In this case, I think replacing reduction="PCA
with reduction.use="pca"
would solve the issue.
Also, I would recommend upgrading to v1.2 because there are fixes and performance enhancements
Thank you so much! I upgraded and changed the parameter to reduction.use
and this did the trick!
Hi all,
Thank you for this amazing package! I have been using it for several years now and it works very well. However, I recently transitioned to a new HPC environment and for some reason I am having problems in running harmony on my dataset. Briefly, I have a dataset of ~1M cells that are both my samples and samples from a public reference that I have combined. I run SCT individually on each sample before merging and running PCA etc (where "orig.ident" is the metadata column corresponding to patient IDs, with 46 patients total):
However, each time it results in the following error.
I confirmed that the PCA is present in the reductions, and that it corresponds to the SCT assay:
Any help in how to solve this would be greatly appreciated! I've been stuck on it for a while now with no avail. Below is the session info: