qc.and.removeDoublets - Githubissues

paiva-s-lab / FlowCT

FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

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qc.and.removeDoublets #8

Closed jozefiendeclercq closed 6 months ago

jozefiendeclercq commented 10 months ago

Hi, I would like to use a FlowCT workflow on my 26-parameter flowcytometry dataset, but I am running into a problem with quality control. When I use the function "qc.and.removeDoublets" function on a SCE object of 27.3 MB (4 fcs files) I get the following error "Error: cannot allocate vector of size 292.4 Gb". I am running the code on a PC with 64.0 GB installed RAM and already increased the R memory available. I noticed that a similar error is generated when running the "flow_auto_qc()" function from the flowAI package. How can I resolve this problem? Thanks!

jgarces02 commented 10 months ago

Hi @jozefiendeclercq, I'll respond to you ASAP. Thanks for your patience!

mlorenzm commented 9 months ago

Hello, I don't know if this issue is still relevant, Or if @jgarces02 already fixed this issue. FWIW, I would try the following:

Ensure that you are using R x64 version (I suppose that you are using a x64 machine, as x32 windows cannot use more than 4GB of memory, please confirm this by checking your system's settings). To check R version go to Tools>Global options (within RStudio), you will find: [64-bit] path/to/your/R
It may be useful to remove anything you don't need on your environment (with rm()), then run gc() (R's garbage collector) before calling qc.and.removeDoublets function, as you may have unused memory generated by tinkering in the same R session.
I assume you already did something in the lines of this solution, but running memory.limit(99999999999999) and restarting R might help.
It seems that it might be a problem of fcs files preprocessed in FlowJo

jgarces02 commented 8 months ago

Sorry, I closed it by error....

Hi all (and sorry for the delayed response). I haven't got time yet to get into this problem, my sincere apologies for that. I'm a new postdoc in another institution at the moment, and this is eating up a bit of my time. I'll try to get it fixed by Christmas, as the Baby Jesus' gift 🤞🏻 Thanks for your patience.

mortadelo93 commented 8 months ago

Same issue here, but removing Time parameter from the FCS files it works, although some warnings appear. I worked with FCS3 files exported from FlowJo.

jgarces02 commented 8 months ago

Hi all,

Please, try to install the last version of flowAI and let me know if it works well (BiocManager::install("flowAI")).

Also, did you have any problem like this using the tutorial files? I cannot reproduce the error.

Thanks

mortadelo93 commented 7 months ago

I re-installed flowAI and now when running qc.and.removeDoublets() with all markers the session is aborted... Still, if a I remove Time parameter from data it works. Not a big issue anyway.

jgarces02 commented 6 months ago

Should I understand that removing the parameter Time is enough?

mortadelo93 commented 6 months ago

At least in my case that worked. It makes event cleaning based on other physical parameters.