HelenaLC
commented
1 year ago Hm, I haven't worked with data that large / this many events, so not sure. (Also, sorry for my ignorance, but what is XT data and why would you assume this might be the cause?) In any case, may I suggest debarcoding in chunks (e.g., a couple million events at a time). Then, a significant proportion of the data could be dropped via filtering out unassigned events. And, lastly, cells mapped to a sample could be concatenated back into a single object?
Hi
I am trying to debarocde some cytof data. For a third of the some datasets it works nicely, however for some samples I get an R core-dump. The datasets have between 20-50 million events, and I don't get any errors when reading in the data in R. My desktop has 128 GB of ram so should be more than enough for debarcoding this data.
The only thing we can think might be a problem is that this is XT data.
R commands:
sce <- prepData( raw_dir, transform=TRUE ) sce <- assignPrelim(sce, sample_key) sce <- estCutoffs(sce) sce_specific <- applyCutoffs(sce)
R error:
caught segfault address 0x7ec2c5614740, cause 'memory not mapped'
Traceback: 1: vapply(seps, function(u) x$delta >= u, numeric(ncol(x))) 2: estCutoffs(sce) An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)