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TIMESTEP for Cytof data

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CostaVUmc

Participant

Posts: 1

Joined: Fri Jun 01, 2018 8:59 am

Post Tue Jun 05, 2018 6:49 am

TIMESTEP for Cytof data

I would like to apply the flowAI package on my cytof data for automated removal of flow rate anomalies. FlowAI requires the $TIMESTEP parameter to do this, but this is not included in the headers of .FCS files that I obtain. I can add it myself in R.

Does anyone have a proper strategy for this? What is a proper value to add? Is this fixed for Cytof data?

I would appreciate some expert suggestions.

Many thanks in advance,

Costa
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BjornZ

Contributor

Posts: 33

Joined: Fri Jul 10, 2015 1:04 am

Post Wed Jun 06, 2018 3:33 am

Re: TIMESTEP for Cytof data

Hi Costa -- I think the correct value is 0.001 (that is, one TIME unit is 1 millisecond). That gives reasonable values for data I just looked at from a Helios and CyTOF2.
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XMUCyTOF

Participant

Posts: 7

Joined: Tue Aug 07, 2018 3:09 am

Post Sat Aug 17, 2019 1:08 am

Re: TIMESTEP for Cytof data

BjornZ wrote:Hi Costa -- I think the correct value is 0.001 (that is, one TIME unit is 1 millisecond). That gives reasonable values for data I just looked at from a Helios and CyTOF2.

Hi,
I'm also trying the script, and I followed your suggestion by setting the second_fractionFR = 0.001. But it shows " The argument second_fractionFR must be greater or equal to timestep".
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Mon Aug 19, 2019 7:33 am

Re: TIMESTEP for Cytof data

I can't help with the flowAI, but I can also confirm that 1ms is correct.

I've written a script that plots FCS data vs. time and my script implements 10 ms units for flow data and 1 ms units for CyTOF data.

The results are correct for BD instruments (Canto, Aria) and CyTOF 2 and 3 (Helios) - i.e. the event rate and total acquisition duration are correct in each case.
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XMUCyTOF

Participant

Posts: 7

Joined: Tue Aug 07, 2018 3:09 am

Post Mon Aug 19, 2019 7:39 am

Re: TIMESTEP for Cytof data

jimbomahoney wrote:I can't help with the flowAI, but I can also confirm that 1ms is correct.

I've written a script that plots FCS data vs. time and my script implements 10 ms units for flow data and 1 ms units for CyTOF data.

The results are correct for BD instruments (Canto, Aria) and CyTOF 2 and 3 (Helios) - i.e. the event rate and total acquisition duration are correct in each case.


Great, Could you please share your script with me? I'd like to have a try because I'm using the FlowJo plunges but it seems strange.
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jimbomahoney

Master

Posts: 73

Joined: Wed Feb 27, 2019 11:21 am

Post Mon Aug 19, 2019 8:11 am

Re: TIMESTEP for Cytof data

Sure - please excuse the probably messy code! I'm new to R and cytometry!

https://github.com/JimboMahoney/CytobankGraphs
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XMUCyTOF

Participant

Posts: 7

Joined: Tue Aug 07, 2018 3:09 am

Post Mon Aug 19, 2019 8:19 am

Re: TIMESTEP for Cytof data

jimbomahoney wrote:Sure - please excuse the probably messy code! I'm new to R and cytometry!

https://github.com/JimboMahoney/CytobankGraphs

Thank you so much, I'll try it.

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