FCS3 Files Exported from FlowJo 10.0.7 are incompatible with citrus

[ccheste1]

My FCS files gates for live, intact, singlets and exported out of FlowJo 10.0.7, when loaded into Citrus, generate the following error during the initial reading of the FCS file parameters:

" Error in value[3L] : Unexpected Error: Error in value[3L]: Parameter(s) $BEGINDATA not contained in 'x' "

It appears that somehow in the export process through FlowJo 10.0.7 the $BEGINDATA parameter is lost and the file becomes unrecognizable to citrus. Any suggestions on how to remedy?

Thanks, Cariad

[rbruggner]

Hi Cariad,

Have you confirmed that the keyword is present before processing the data in flojo and then missing afterwards?

Has the data been processed using any other utilities, including de-barcoding, normalization, concatenation scripts, etc?

Cheers

Rob

On Aug 21, 2014, at 6:18 PM, Cariad notifications@github.com wrote:

My FCS files gates for live, intact, singlets and exported out of FlowJo 10.0.7, when loaded into Citrus, generate the following error during the initial reading of the FCS file parameters:

" Error in value[3L] : Unexpected Error: Error in value[3L]: Parameter(s) $BEGINDATA not contained in 'x' "

It appears that somehow in the export process through FlowJo 10.0.7 the $BEGINDATA parameter is lost and the file becomes unrecognizable to citrus. Any suggestions on how to remedy?

Thanks, Cariad

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[ccheste1]

Hey Rob,

I have confirmed that the data, pre FlowJo X processing, is compatible with citrus. But, after FlowJo X export, the $BEGINDATA keyword is removed. When checking the post-FlowJo X export files using the FileParameterConsistency feature, you get the same missing $BEGINDATA error that loads when citrus attempts to run analysis using the files: " Reading parameters in 12-c1-st-live.FCS3.fcs Error in value[3L] : Parameter(s) $BEGINDATA not contained in 'x' "

The files have not been subjected to de-barcoding, normalization, or concatenation. Have other users been able to seamlessly export using FlowJo X?

Thanks, Cariad

[rbruggner]

Unfortunately, there's not a lot I can do on my side of things. If flowCore (the R package used to read / write FCS files) can't read the FCS files at all (which it doesn't appear to be able to), I can't really do anything to fix them.

However, I'm a little surprised that FlowJo X is writing the files wrong, especially considering how mainstream the program is (and the fact that they list BEGINDATA as a required keyword here).

It would definitely be worth filing a support ticket with them to figure out what's going on because I think this is a rather big problem if its indeed missing that keyword during export.

I'm going to close this ticket for now since I don't think there's anything I can do on my end but feel free to post again if you find some sort of resolution.

[michaelmior]

@ccheste1 Were you able to resolve this issue on the FloJo side? I just came across this after investigating a similar problem and it would be great to hear if you found a solution.

[ccheste1]

Unfortunately, this issue has not been resolved. The problem has been communicated to the FlowJo support team and they have said they "hope" to address it in the 2015 upgrade of FlowJo X. I would vote for you calling them to keep it on their radar, but in the interim I'm using FlowJo version 9.

[rbruggner]

Someone from Mark Davis' group has allegedly patched flowCore to work with the broken fcs files. I will try and get him to post a how to for the fix.

On Sep 23, 2014, at 2:15 PM, Cariad notifications@github.com wrote:

Unfortunately, this issue has not been resolved. The problem has been communicated to the FlowJo support team and they have said they "hope" to address it in the 2015 upgrade of FlowJo X. I would vote for you calling them to keep it on their radar, but in the interim I'm using FlowJo version 9.

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[jpabbuehl]

Hi everyone, thank you for your package. I am also running into the same problem as everyone here (FCS exported from FlowJo after excluding live, intact, singlets missing $BEGINDATA). Have you found a temporary fix ?

[rbruggner]

Some of the maintainers of the flowCore package have rolled in a temporary fix, although this is not currently available in bioconductor. However, you can install a patched version of flowCore directly from github and that should allow you to read those broken files.

To install flowCore directly from github (in R):

R> library("devtools")
R> install_github("RGLab/flowCore",dependencies=NA)

I would still encourage you to write to flowJo and ask them to correct the issue.

[jpabbuehl]

Thx. This solved my issue