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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Error Downsampling #64

Closed dougalld closed 11 years ago

dougalld commented 11 years ago

Similar to other comments, I am using a pre-gated FlowJo file (FlowJo v9.6.4). Note: flowJo exported the file in fcs 2.0 format.

I get the following error: Error in fcs_text_parse(txt, emptyValue = emptyValue) : No end found There could be double delimiter existing in keyword value. Please set argument 'emptyValue' as FALSE and try again! Calls: SPADE.driver -> SPADE.downsampleFCS -> SPADE.read.FCS Execution halted

Thoughts? Could this be "Dump/CD123" being used as a channel name?

rbruggner commented 11 years ago

This is related to flowCore in R not being able to deal with empty values in keywords. Usually, this is because the parameter name or description keys ($PxN) are in the FCS file but no value is specified. If you export to FCS 3.0, does this fix the problem?

On Jun 12, 2013, at 9:36 AM, dougalld notifications@github.com wrote:

Similar to other comments, I am using a pre-gated FlowJo file (FlowJo v9.6.4). Note: flowJo exported the file in fcs 2.0 format.

I get the following error: Error in fcs_text_parse(txt, emptyValue = emptyValue) : No end found There could be double delimiter existing in keyword value. Please set argument 'emptyValue' as FALSE and try again! Calls: SPADE.driver -> SPADE.downsampleFCS -> SPADE.read.FCS Execution halted

Thoughts? Could this be "Dump/CD123" being used as a channel name?

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zbjornson commented 11 years ago

In addition to rbruggner's comment and as you suggested, slashes ("/") are commonly used as delimiters in FCS file headers and rarely handled properly by FCS readers/writers. You could try changing that to a different character.

dougalld commented 11 years ago

I tried exporting into fcs 3.0 format and got a different error:

Downsampling file: ./SYS99_pregate_4spade_FCS3.fcs Error in exprs(ff) : error in evaluating the argument 'object' in selecting a method for function 'exprs': Error in readFCSgetPar(x, "$BEGINDATA") : Parameter(s) $BEGINDATA not contained in 'x' Calls: SPADE.read.FCS Calls: SPADE.driver ... SPADE.addDensityToFCS -> SPADE.transform.FCS -> apply -> exprs Execution halted

rbruggner commented 11 years ago

In that case, give Zach's suggestions a try?

On Jun 12, 2013, at 9:45 AM, dougalld notifications@github.com wrote:

I tried exporting into fcs 3.0 format and got a different error:

Downsampling file: ./SYS99_pregate_4spade_FCS3.fcs Error in exprs(ff) : error in evaluating the argument 'object' in selecting a method for function 'exprs': Error in readFCSgetPar(x, "$BEGINDATA") : Parameter(s) $BEGINDATA not contained in 'x' Calls: SPADE.read.FCS Calls: SPADE.driver ... SPADE.addDensityToFCS -> SPADE.transform.FCS -> apply -> exprs Execution halted

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