[Cytometry] Conversion into FCS File and vice versa
COSMA Antonio 224446
antonio.cosma at cea.fr
Fri Feb 26 11:44:33 EST 2010
Let me resume if I understood well.
FCS3 file are binned internally in FlowJo to a 0 to 4096 scale.
We can say Channel can assume 4096 different values.
Scale value are expressed as floats but can only assume 4096 different values, since resolution is the same.
I plotted scale value and channel value with excel and I imagine FlowJo uses scale value to create his plots? Am I right?
Do you know have some documentation about this process?
From: Maciej Simm [mailto:simm at treestar.com]
Sent: lundi 22 février 2010 18:45
To: COSMA Antonio 224446
Cc: cytometry at flowcyt.cyto.purdue.edu
Subject: Re: [Cytometry] Conversion into FCS File and vice versa
to answer, let me first define the terms as I understand them.
Scale values refer to magnitude of your events along a parameter, as you would see them in a graph window.
Channel values refer to how the data is organized inside the file, and may or may not be the same number as you would derive from looking at a plot.
The discrepancy comes from the fact that some legacy data (FCS2, analog files) has values written out in 1024 "channels" but presented to the user on a 1-10000 "scale" (usually on a 256 pixel plot, but I digress.)
Channels are usually integers, while scale values are usually floats.
Most of the data being output by current cytometers I've looked at is in FCS3 format, and is written and shown in "channel" - therefore the distinction is no longer necessary. This issue is only relevant when examining legacy FCS2 data. There is, however, a kink - FlowJo reads in data files and bins them internally to a 12 bit resolution. Therefore the highest possible "channel" resolution we can currently report is on a 0-4096 scale ( as integers.) Using "scale" option would yield the same precision but present the data as floats.
So, which is better? they're the same - but if you prefer to work with Integers, go with Channel. ;)
On 21 Feb 2010, at 12:20, COSMA Antonio 224446 wrote:
> Dear Maciej,
> I have an opposite questio:
> I am extracting list mode files from FlowJo to perform cluster analysis.
> When I go to the Export windows in FlowJo, I have two option for exporting:
> Channel numbers
> Scale values
> Which is the best according to you? Which are the advantages and disadvantages for each system?
> Antonio Cosma
> Service d'Immuno-Virologie
> Commissariat à l'Energie Atomique
> 18, route du Panorama
> 92265, Fontenay-aux-Roses, Cedex
> Tel: +33-1-46 54 82 84
> Fax: +33-1-46 54 77 26
> -----Original Message-----
> From: cytometry-bounces at lists.purdue.edu
> [mailto:cytometry-bounces at lists.purdue.edu] On Behalf Of Maciej Simm
> Sent: vendredi 19 février 2010 17:41
> To: Joel M. Sederstrom
> Cc: cytometry at flowcyt.cyto.purdue.edu
> Subject: Re: [Cytometry] Conversion into FCS File
> I'll add a video tutorial to that URL over the weekend to better explain how it works.
> Maciej Simm
> FlowJo/Daily Dongle
> On 19 Feb 2010, at 06:21, Joel M. Sederstrom wrote:
>> The Daily Dongle had a conversion using FlowJo. I am still trying to
>> wrap my head around it though.
>> I am interested in this so please share any direct correspondence if
>> you would.
>> Joel M. Sederstrom, M.S.
>> Director, Cytometry and Cell Sorting Core Baylor College of Medicine
>> Phone: 713.798.3774
>> email: sederstr at bcm.edu
>> On Thu, Feb 18, 2010 at 1:09 PM, Nastaran Hashemi <nastaran at vt.edu> wrote:
>>> Dear All,
>>> I would like to convert an excel file containing flow cytometry data
>>> into a .fcs file for further data analysis. I was wondering if you
>>> know of any software that can used for this kind of conversion or
>>> have any idea on how to write a code in order to convert my excel files.
>>> Thanks for your help.
>>> Nastaran Hashemi, PhD
>>> Center for Bio/Molecular Science & Engineering
>>> Naval Research Laboratory
>>> Washington, DC 20375
>>> <nastaran.hashemi.ctr at nrl.navy.mil>
>>> (202) 767-2147
>>> Cytometry mailing list
>>> Cytometry at lists.purdue.edu
>> Cytometry mailing list
>> Cytometry at lists.purdue.edu
> Maciej Simm
> Director of Science
> Tree Star Inc.
> Cytometry mailing list
> Cytometry at lists.purdue.edu
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