Memory usage
BradleyH017 opened this issue · comments
Hi Chris,
Thanks for the great paper and easy to follow analysis.
I want to repeat this but using all healthy samples (not just the 10 in the training set). I have tried using run_analysis.r but with all cells of each subset. This is fine until ComBat batch correction, at which point this fails due to a memory error, regardless of how much memory I request for my R session.
I have also tried running as a DelayedArray, but this still fails. Presumably this is because the data is still being read to disk by the ComBat function.
I was wondering if you could shed some light on how much memory you are using to run this analysis, or how you overcame this.
Thanks for your help,
Bradley
Hi Bradley,
Were you able to resolve this?
I'm running into the same issue.
Thanks!
Maarten
Hi Maarten,
Not using ComBat. I gave Harmony a go, but using reciprocal integration from Seurat gave me the best looking results batch-wise.
Best,
Bradley