error modeling knn takes up all cores about scde HOT 9 OPEN

from scde.

Here is the command:
knn <- knn.error.models(cd_new_nodup, k = ncol(cd)/2, n.cores = 12, min.count.threshold = 1, min.nonfailed = 20, max.model.plots = 10)

dim of the matrix is ~ 13k genes but 4k cells. I've filtered out any genes that have no expression.

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This is UMI data also

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from scde.

Ok, I will try this. On the scde help page it says that k may need to be increased for 1000s of cells, which is why I kept the denominator low.

Can't run that command because the pagoda library is not installed apparently. I thought it was installed along with SCDE package?

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When running scde:::papply( 1:1e2, function(x) rnorm(1e3), n.cores=12)
It finishes in about 2 seconds, and can't tell the core usage.

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after increasing rnorm, it seems to be running on 12 cores only.

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While the scde:::papply( 1:1e2, function(x) rnorm(1e3), n.cores=12) runs on only 12 cores, the knn parameter still uses all cores.

Any ideas on why the discrepancy?

from scde.