Question

ncdfFlowSet with dim=3

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anders.tondell ▴ 30

@anderstondell-9441

Last seen 3.4 years ago

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

ncdfflow flow cytometry • 1.1k views

ADD COMMENT • link updated 5.2 years ago by Jiang, Mike ★ 1.3k • written 5.2 years ago by anders.tondell ▴ 30

score 1 · Answer 1 · 2019-01-31

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Jiang, Mike ★ 1.3k

@jiang-mike-4886

Last seen 2.5 years ago

(Private Address)

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

ADD COMMENT • link 5.2 years ago Jiang, Mike ★ 1.3k

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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

ADD REPLY • link 5.2 years ago anders.tondell ▴ 30

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Glad to hear! Thanks for reporting the issue.

ADD REPLY • link 5.2 years ago Jiang, Mike ★ 1.3k