Error when using read.FCS
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Pepijn • 0
@85919942
Last seen 8 months ago

Hello everyone,

I'm trying to read my FCS file of spleen data into R, but I'm getting this error. I exported the FCS file with the compensated parameters from Flowjo. If I export the uncompensated data from Flowjo, it reads the FCS without any errors. I'm a student that is quite new to this, so I sadly can't provide you with alot of details. I wondered if anyone knew how I could fix this error.

myfile <- "D:/BPS/RP1/Autogating/Databank/test2.fcs"
fcsfile <- read.FCS(myfile)

Error in string_to_spill(txt) : 
  bad lexical cast: source type value could not be interpreted as target
In addition: There were 50 or more warnings (use warnings() to see the first 50)
compensation flowCore FlowCore read.FCS • 180 views
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SamGG ▴ 270
@samgg-6428
Last seen 8 weeks ago
France/Marseille/Inserm

Hi,

You should select a FCS 3.0 as file format and export all uncompensated channels. The compensation matrix is saved within the FCS, so that you could easily compensate the data when reading the FCS file in R.

More on that in paragraph 5 of the flowCore vignette.

The current error states that the compensation/spillover matrix has an unattended shape for read.FCS function.

Best.

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