Panel Editor truncating data values

[rehamlin]

Hello,

I am using Premessa's Panel Editor GUI on a set of CyTOF FCS files to harmonize the channel names. I have already concatenated, normalized, debarcoded, and gated/exported new .fcs files from FlowJo on live, single, CD45+ cells.

The Panel Editor is giving warnings for many channels that say, for example:
"Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'Dy161Di' channel exceed its $PnR value 1 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'"

Since it's a GUI, I can't change the code to set 'truncate_max_range = FALSE'". If I look at the new renamed fcs file in FlowJo, it is literally truncated at 1.

I also tried using cytofCore.updatePanel, and I experienced the same issue.

Does anyone know if there's a way to get around this in the panel editor? or perhaps I'm exporting the live, single, CD45+ cell fcs files incorrectly from FlowJo that could be leading to this issue? Or is there code for a panel editor I could use, so I could include 'truncate_max_range = FALSE'" to try to get around this?

Thanks in advance for any help!

Best,
Rebecca

[sgranjeaud]

Hi,

I already sent this answer by email but it didn't reach cytoforum.

First, I would like to thank Frederico for its.

While waiting the official patch from Frederico, I updated a fork of Premessa.

Just install it with

  Code:

library(devtools)
install_github("i-cyto/premessa")


I have no time to test, so use it with care and send me feedback off-line.

I integrated changes from cphealy8 concerning the file name pattern and BOM removal, nice ones.

Hope this help,
Samuel

[rehamlin]

Thanks for your reply. Prior to receiving this, I did get around the issue by doing panel editor prior to gating in FlowJo/exporting new FCS files, and this seemed to bypass the issue. The values were no longer truncated when I did panel editor first.

[sgranjeaud]

Thanks for your feedback. It's important to let a track in this forum in the case someone faces the same question.

For curiosity... In your previous trial, it seems that FJ was writing FCS files that raise truncation warnings in Premessa (in fact flowCore). In your current worflow, FJ is also the last program to write FCS files. If you reopen these FCS with Premessa, do you encounter truncation warnings?

Best.

[rehamlin]

I just tested this by importing my flowjo exported FCS files (upon which I had previously used panel editor prior to flowjo gating/exporting) into Premessa panel editor and removed one of the channels as a test. This time I did not get truncation error messages. I then looked at the newly panel edited FCS files in FlowJo, and they are not truncated!

Best,
Rebecca

[sgranjeaud]

Well, not conclusive. Thanks a lot for your feedback and time.
Best,
Samuel

[juliam]

Hi There,
I came across panel editor truncating values.

I have seen that to avoid this problem we can unify the panel on RAW FCS files before any gating.

The template for unifying seems to have problems as it doesn't have some metals which I ma using like In115 or Pt194.
From where to take most recent panel template? (if I don't want to use FCS file as a template (which seems to have way more problems)
Thanks!

Julia