ncdfFlowSet with dim=3
1
1
Entering edit mode
@anderstondell-9441
Last seen 2.2 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 • 760 views
1
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 16 months ago

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

1
Entering edit mode

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

0
Entering edit mode

Glad to hear! Thanks for reporting the issue.