Time data is logicle transformed

[GoogleCodeExporter]

What steps will reproduce the problem?
1. load an FCS file

What is the expected output? What do you see instead?

I expect the time data to always be linear.
Instead the time data is automatically transformed with a logicle transformation

What version of the product are you using? On what operating system?

0.9.1

Please provide any additional information below.

I suspect that the location in the source code that should take care of this is:

in readfcs.py in the get_FCMdata function. Line '94':

                if name != 'Time':
                    scchannel_indexes.append(i - 1)

The problem is that the FCS file I have has the name 'HDR-T' for the time 
channel:

(e.g., the fcs text is: 'p1n' : 'HDR-T')

I am using a MacsQuant cytometer.
The annotation provided with it in the fcs file is the following:
'sys': 'MACSQuantify,2.4.1247.1dev'
'cyt': 'MACSQuant'

I attached a sample FCS file from my flow cytometry machine.

Original issue reported on code.google.com by eyurt...@gmail.com on 15 Apr 2013 at 6:29

Attachments:

• test.py
• EY_2013-04-14_EID_201_PID_1030_Penicillin_G_Well_H9.001.fcs

[GoogleCodeExporter]

Thanks, I'll look into if there's a more consistent way of labeling time 
channels.

Original comment by Jacob.Frelinger@gmail.com on 17 Apr 2013 at 12:33

• Changed state: Accepted