Question: ncdfFlowSet with dim=3
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7 months ago by
anders.tondell30 wrote:

I am currently working with a ncdfflowset from a large number of fcs-files (>1500).

I need to set several keywords to NA, but it seems changing keywords on this large ncdfflowset are extremely time-consuming (~30 sec. pr. sample). However, on subsets of the ncdfflowset object with 100 samples (FCS-files) the time used pr. sample is 1/10 as long.

keyword(ncfs) <- list(EXPERIMENT NAME=NA, $SRC=NA, $FIL=NA,\$FILNAME=NA)

Is there any way to make this code more effective. The documentation on read.ncdfFlowSet is a bit scarce. What is the pros and cons of 'dim=3'?

Thanx in advance for any suggestions,

Anders T

flow cytometry ncdfflow • 296 views
modified 7 months ago by Jiang, Mike1.2k • written 7 months ago by anders.tondell30
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7 months ago by
Jiang, Mike1.2k
Jiang, Mike1.2k wrote:

see the solution here https://github.com/RGLab/ncdfFlow/issues/44#issuecomment-459527469

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Thank you so much, this is excellent! A test on our university system on a 200 frames ncdfFlowset: keyword changed instantly on the whole ncdfFlowset! I can't see why anyone would use any other flow cytometry software.

Anders T