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FlowCAP 2 data
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Noah Zimmerman  
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 More options Jul 12 2011, 11:42 pm
From: Noah Zimmerman <no...@stanford.edu>
Date: Tue, 12 Jul 2011 20:42:56 -0700
Local: Tues, Jul 12 2011 11:42 pm
Subject: FlowCAP 2 data
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Greetings,

I noticed that the data for the FlowCAP-2 challenges are available as either raw FCS files or pre-transformed and pre-compensated CSV files. I looked in the header of several of the data files for challenge #1 and didn't find a spillover matrix. Will you provide the appropriate compensation matrix(ces) so that we can compensate the FCS files ourselves?  For those people using the transformed/compensated CSV files, can you provide details on what transformations you used (and any parameters you set for those transformations)?

Thanks!
Noah Zimmerman  


 
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Nima Aghaeepour  
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 More options Jul 13 2011, 12:22 pm
From: Nima Aghaeepour <nni...@gmail.com>
Date: Wed, 13 Jul 2011 09:22:36 -0700
Local: Wed, Jul 13 2011 12:22 pm
Subject: Re: [flowCAP] FlowCAP 2 data
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Hi Noah,

Re. compensation:
Thanks for brining this to our attention. I'll contact the lab that has
produced the data to get the compensation information and will get back to
you.

Re. transformation:
We have used an R package that has Wayne Moore's implementation of Logicle
(W=0.5, M=4.5, A=0, bins=0)

Cheers,
Nima.


 
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Nima Aghaeepour  
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 More options Jul 14 2011, 5:36 pm
From: Nima Aghaeepour <nni...@gmail.com>
Date: Thu, 14 Jul 2011 14:36:11 -0700
Local: Thurs, Jul 14 2011 5:36 pm
Subject: Re: [flowCAP] FlowCAP 2 data
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Dear FlowCAP2 participants,

We fixed two problems:

-The CSV files for HEUvsUE are now compensated correctly. You can redownload
the files or download the spillover matrices from here:
http://www.terryfoxlab.ca/flowsite/FlowCAP2/download/HEUvsUE/Compensa...

-Some of the CSV files for the HVTN challenge were problematic. The files
are fixed in the version available online.

Cheers,
Nima.


 
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