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Concatenating FCS files

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komal2000

Participant

Posts: 16

Joined: Mon Aug 29, 2016 12:55 pm

Location: University of Helsinki, Finland

Post Thu Sep 17, 2020 8:23 am

Concatenating FCS files

Dear All,'

I profiled immune cells at diagnosis and after treatment and I also grouped patients into Good and bad responders . Wanted to concatenate fcs files from all the good responders and bad responders separately. In cytobank it is not possible. Is it possible to do it in flowjo?, any other suggestions? Keep in mind that I am wetlab scientist.



Sincerely
Komal
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Abhishek

Participant

Posts: 5

Joined: Thu Nov 15, 2018 1:30 pm

Location: Stanford, CA

Post Thu Sep 17, 2020 8:45 am

Re: Concatenating FCS files

Hi Komal,

Check out this link from FlowJo: https://flowjo.typepad.com/the_daily_do ... eters.html

Best,
Abhishek
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Thu Sep 17, 2020 12:23 pm

Re: Concatenating FCS files

Why do you want to concatenate all of the patients into one files?
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avinash1

Participant

Posts: 16

Joined: Fri Jun 16, 2017 1:59 pm

Post Thu Sep 17, 2020 1:32 pm

Re: Concatenating FCS files

Hi Komal

We do it regularly in Flow Jo. However, I would recommend to filter out the beads, DNA negative, doublets and CD45-ve (if it is not a priority for your research) before concantenation. You can do this filtration on cytobank. We do this concatenation to compare biological groups/controls within our study cohort.

Cheers
Avi
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tomaskalina

Participant

Posts: 10

Joined: Fri Dec 20, 2013 9:19 am

Post Fri Sep 18, 2020 7:30 am

Re: Concatenating FCS files

Hi Komal,

very easy to do in FlowJo 10, the gates made in the .wsp can be used by
your computer scientists in R. Remember you can add parameters in this
step in FlowJo "add parameters" that will denote your good vs bad
responders and many more characteristics for any caculations.

Depending on your downstream plans, you may not need to concatenate in
FlowJo, but rather just put all your files there, make the wsp and pass
it to the R scripts of your colleagues.

Best regards, Tomas
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komal2000

Participant

Posts: 16

Joined: Mon Aug 29, 2016 12:55 pm

Location: University of Helsinki, Finland

Post Fri Sep 18, 2020 7:38 am

Re: Concatenating FCS files

Hi Thanks Abhishek, Avinash, and Tomas. Yes, I did it in Flowjo for now, need to look at the data. I am also looking OMIQ software, trying free trial.
Answer to Amir question: I am comparing good and bad responders in bulk just for curiosity.



Sr
Komal

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