Error reading exported FlowJo files

[hhopp]

Hello,

I exported some manually gated data from FlowJo, and am having trouble getting SPADE to read it.

I get this error:

Error in readFCSgetPar(x, "$BEGINDATA") :
Parameter(s) $BEGINDATA not contained in 'x'

I assume this is an issue with FlowJo's exporting. It seems this was addressed here: http://permalink.gmane.org/gmane.science.biology.informatics.conductor/20229
However, I am not sure how to patch SPADE so that this error doesn't pop up again.

Thank you for your help.

[rbruggner]

This is a slightly different issue wherein flojo appears to be incorrectly omitting the BEGINDATA keyword from fcs files during export.

See: nolanlab/citrus#72

I highly encourage you to contact them and ask them to fix the problem as this causes trouble for all R-based tools.

On Sep 18, 2014, at 4:25 PM, hhopp notifications@github.com wrote:

Hello,

I exported some manually gated data from FlowJo, and am having trouble getting SPADE to read it.

I get this error:

Error in readFCSgetPar(x, "$BEGINDATA") :
Parameter(s) $BEGINDATA not contained in 'x'

I assume this is an issue with FlowJo's exporting. It seems this was addressed here: http://permalink.gmane.org/gmane.science.biology.informatics.conductor/20229
However, I am not sure how to patch SPADE so that this error doesn't pop up again.

Thank you for your help.

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Reply to this email directly or view it on GitHub.

[rbruggner]

Workaround posted here: nolanlab/citrus#72